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/%] ] 3study_AIGERP002474Adineta_vaga_cdnaMetagenomicsTranscriptome sequencing of Adineta vagaGSCAIGTranscriptome sequencing of Adineta vagaLinked publication: http://dx.doi.org/10.1038/nature12326ERA2069992016-11-20 16:45:05�( # � �i% � �i �9 3�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585ERA2037992016-11-20 16:45:02�B ! K %+K� �5 3�E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherArrayExpressGATC Biotech AGwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861ERA0708432016-11-20 16:44:06�
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~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisArrayExpressAAUTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552pubmed: 21743474ERA0215692016-11-20 16:43:56�t ! G %+G�m �O 3 �E-MTAB-387ERP000350RNA sequencing in E. coli K12OtherArrayExpressEMBL_HeidelbergRNA sequencing in E. coli K12Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phaseE-MTAB-387 in ArrayExpress: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MTAB-387ERA0141842016-11-20 16:43:52�9� �s9? �s�K 3 �Identification of the expression profile of Staphylococcus aureus grown in the presence or absence of a fatty acid. -sc-2010-06-07ERP000233Identification of the expression profile of Staphylococcus aureus grown in the presence or absence of a fatty acid.Transcriptome AnalysisLink to project web page.SCIdentification of the expression profile of Staphylococcus aureus grown in the presence or absence of a fatty acid.Transcriptome analysis of two strains of S. aureus (SH1000 and EMRSA 16) under two growth conditions. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ERA0089872016-11-20 16:43:49�[ a9�E !5�? 3
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.OSAKA_PREFSolanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.DRA0035282017-09-21 20:27:47
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� *�� �b# ]�O ! 3��PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism.BioProjectSRA6023132017-08-24 20:07:03�r; �Q� ?3 - 3DTrout transcriptome-454SRP001007Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesOtherBackground: Rainbow trout is important fish species for aquaculture and biomedical research but has no genomic data. Until genome sequence becomes available, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Large-scale EST (258,973) Singer sequences are publicly available for rainbow trout. However, the nature of duplicated rainbow trout genome hinders assembly and annotation of the EST sequences. Additionally, previous efforts aimed at SNP discovery for rainbow trout using ESTs were unsuccessful, mainly, due to difficulties parsing allelic variation from the high frequency of duplicated genes. Results: High-throughput shotgun deep sequencing of the rainbow trout double-haploid transcriptome using DNA 454-pyrosequencing technology has been successfully applied yielding about 1.3 million reads with an average length of 344bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus sequences (TCs) (Average length 662 nt) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing Singer sequences resulted in 161,818 TCs (Average length 758 nt) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed similarity to the expected transcriptome of other fish species with known genome sequences, suggesting a genome-wide representation of the rainbow trout transcriptome sequence. Conclusion: The 454 library added great amount of new EST sequences and identified new genes. In addition, it improved assembly and annotation of the rainbow trout Sanger EST. The 454 library is a new tool for functional genome research in rainbow trout. It provides a reference sequence to identify gene duplications, allelic variations; distinguish true/false SNPs as well as for digital gene expression and proteomic research in rainbow trout.West Virginia University,Oncorhynchus mykisspubmed: 20942956SRA0092762016-11-20 16:51:03�f9 C�y % - I 3C�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.BIHomo sapienspubmed: 20179022parent_bioproject: PRJNA118501SRA0090532017-09-21 20:38:11�j! o;�k �+ G 3>�2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.WUGSCStreptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331SRA0002462017-01-26 20:08:16
� ��� � �?9�# 3ʻGSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGEOGSE104177SRA6125722017-10-12 21:29:04� # �1;�7 !% 3�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.BioProjectHomo sapiensSRA6047562017-09-07 20:02:00�r# � � !! 3�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.BioProjectArtocarpusSRA6047522017-09-07 20:02:00
� ��� �P e�# 3�GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GEOGSE104711SRA6177832017-10-12 21:29:13�# �M�A !% � 3��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)BioProjectHomo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614SRA6157162017-10-19 20:06:45�E �99� 3ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGEOGSE104193SRA6126182017-10-12 21:29:04
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GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GEOGSE104734SRA6179122017-10-12 21:29:14�4 �%9� 3� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GEOGSE104725SRA6178872017-10-12 21:29:14�5 �/9� 3�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GEOGSE104716SRA6178422017-10-12 21:29:14�R �E9�# 3�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GEOGSE104714SRA6178092017-10-12 21:29:13
� e %� > 3�SRP133088SRA6603742018-03-01 17:52:59> 3 �SRP132698SRA6587132018-02-22 17:53:22� �9�m 3�GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGEOGSE104738SRA6179162017-10-12 21:29:14
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A �+ 3Q�DRS019417DRS019417MIYAZAKI�Bursaphelenchus xylophilussex: mix || strain: Ka4C1 || sample_title: B. xylophilus mixed-stage || description: B.xylophilus mixed-stage on B. cinerea || sample_name: BxMixed || bioproject_id: PRJDB3458 || dev_stage: mixed propagativeDRA0029922016-11-20 05:21:49�) - � 3H5DRS021959DRS021959KYOTO_SCDugesia japonicasex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small riverDRA0027222016-11-20 05:21:26�( - � 3H4DRS021958DRS021958KYOTO_SCDugesia japonicasex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small riverDRA0027222016-11-20 05:21:26�$
- � 3H3DRS021957DRS021957KYOTO_SCDugesia japonicasex: asexual || strain: GI || sample_title: Dj_GI_HB || tissue_type: Head blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small riverDRA0027222016-11-20 05:21:26� /) = 3?DRS005669DRS005669NIVTS �#Allium fistulosumbunching onionMature pseudostem of 'F'DRA0009452016-11-20 05:19:02� /) A 3>DRS005668DRS005668NIVTS �#Allium fistulosumbunching onionMature pseudostem of 'Aka'DRA0009452016-11-20 05:19:02| /) - 3=DRS005667DRS005667NIVTS �#Allium fistulosumbunching onionMeristem of 'Ki'DRA0009452016-11-20 05:19:02{ /) + 3<DRS005666DRS005666NIVTS �#Allium fistulosumbunching onionFlowers of 'Ki'DRA0009452016-11-20 05:19:02� /) ? 3;DRS005665DRS005665NIVTS �#Allium fistulosumbunching onion2-week seedlings of 'Aka'DRA0009452016-11-20 05:19:02z /) ) 3:DRS005664DRS005664NIVTS �#Allium fistulosumbunching onionRoots of 'Aka'DRA0009452016-11-20 05:19:02} /) / 39DRS005663DRS005663NIVTS �#Allium fistulosumbunching onionMeristem of 'Aka'DRA0009452016-11-20 05:19:02� /) 5 38DRS005662DRS005662NIVTS �#Allium fistulosumbunching onionMature leaf of 'Aka'DRA0009452016-11-20 05:19:02�B /) �7 37DRS005661DRS005661NIVTS �#Allium fistulosumbunching onionMixture of nine ;� :�q 9�a 8�T 7�G 6�9 5�+ 4� 3� 2� 1{ 0l /] .W -U ,S +Q *O )M (K 'I &F %D $C #B "A !@ ? > = < ; : 9 8 7 6 4 / '
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A �+ 3Q�DRS019417DRS019417MIYAZAKI�Bursaphelenchus xylophilussex: mix || strain: Ka4C1 || sample_title: B. xylophilus mixed-stage || description: B.xylophilus mixed-stage on B. cinerea || sample_name: BxMixed || bioproject_id: PRJDB3458 || dev_stage: mixed propagativeDRA0029922016-11-20 05:21:49�) - � 3H5DRS021959DRS021959KYOTO_SCDugesia japonicasex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small riverDRA0027222016-11-20 05:21:26�( - � 3H4DRS021958DRS021958KYOTO_SCDugesia japonicasex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small riverDRA0027222016-11-20 05:21:26�$
- � 3H3DRS021957DRS021957KYOTO_SCDugesia japonicasex: asexual || strain: GI || sample_title: Dj_GI_HB || tissue_type: Head blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small riverDRA0027222016-11-20 05:21:26� /) = 3?DRS005669DRS005669NIVTS �#Allium fistulosumbunching onionMature pseudostem of 'F'DRA0009452016-11-20 05:19:02� /) A 3>DRS005668DRS005668NIVTS �#Allium fistulosumbunching onionMature pseudostem of 'Aka'DRA0009452016-11-20 05:19:02| /) - 3=DRS005667DRS005667NIVTS �#Allium fistulosumbunching onionMeristem of 'Ki'DRA0009452016-11-20 05:19:02{ /) + 3<DRS005666DRS005666NIVTS �#Allium fistulosumbunching onionFlowers of 'Ki'DRA0009452016-11-20 05:19:02� /) ? 3;DRS005665DRS005665NIVTS �#Allium fistulosumbunching onion2-week seedlings of 'Aka'DRA0009452016-11-20 05:19:02z /) ) 3:DRS005664DRS005664NIVTS �#Allium fistulosumbunching onionRoots of 'Aka'DRA0009452016-11-20 05:19:02} /) / 39DRS005663DRS005663NIVTS �#Allium fistulosumbunching onionMeristem of 'Aka'DRA0009452016-11-20 05:19:02� /) 5 38DRS005662DRS005662NIVTS �#Allium fistulosumbunching onionMature leaf of 'Aka'DRA0009452016-11-20 05:19:02�B /) �7 37DRS005661DRS005661NIVTS �#Allium fistulosumbunching onionMixture of nine tissues from inbred 'Ki' (2-weeks seedlings, leaf, roots, basal meristem, immature flower bract, mature bract (about 1 week before anthesis), opened flowers, immature fruits and sliced pseudostem).DRA0009452016-11-20 05:19:02
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=Oas� � �k !5 � 3W�DRS019570DRS019570OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time20 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL20 shows 20 hours later with the light. || sample_name: LL20 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�g !5 � 3W�DRS019569DRS019569OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time2 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL2 shows 2 hours later with the light. || sample_name: LL2 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019568DRS019568OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time18 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL18 shows 18 hours later with the light. || sample_name: LL18 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019567DRS019567OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time16 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL16 shows 16 hours later with the light. || sample_name: LL16 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019566DRS019566OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time14 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL14 shows 14 hours later with the light. || sample_name: LL14 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019565DRS019565OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time12 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL12 shows 12 hours later with the light. || sample_name: LL12 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019564DRS019564OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time10 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL10 shows 10 hours later with the light. || sample_name: LL10 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�d !5 � 3W�DRS019563DRS019563OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time0 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL0 shows the moment with the light. || sample_name: LL0 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10
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6HZl~ � �k !5 � 3W�DRS019578DRS019578OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time36 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL36 shows 36 hours later with the light. || sample_name: LL36 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019577DRS019577OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time34 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL34 shows 34 hours later with the light. || sample_name: LL34 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019576DRS019576OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time32 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL32 shows 32 hours later with the light. || sample_name: LL32 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019575DRS019575OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time30 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL30 shows 30 hours later with the light. || sample_name: LL30 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019574DRS019574OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time28 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL28 shows 28 hours later with the light. || sample_name: LL28 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019573DRS019573OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time26 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL26 shows 26 hours later with the light. || sample_name: LL26 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019572DRS019572OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time24 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL24 shows 24 hours later with the light. || sample_name: LL24 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019571DRS019571OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time22 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL22 shows 22 hours later with the light. || sample_name: LL22 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10
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:L^p� � �k' !5 � 3W�DRS019586DRS019586OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time50 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL50 shows 50 hours later with the light. || sample_name: LL50 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k& !5 � 3W�DRS019585DRS019585OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time48 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL48 shows 48 hours later with the light. || sample_name: LL48 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k% !5 � 3W�DRS019584DRS019584OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time46 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL46 shows 46 hours later with the light. || sample_name: LL46 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k$ !5 � 3W�DRS019583DRS019583OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time44 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL44 shows 44 hours later with the light. || sample_name: LL44 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k# !5 � 3W�DRS019582DRS019582OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time42 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL42 shows 42 hours later with the light. || sample_name: LL42 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k" !5 � 3W�DRS019581DRS019581OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time40 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL40 shows 40 hours later with the light. || sample_name: LL40 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�g! !5 � 3W�DRS019580DRS019580OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time4 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL4 shows 4 hours later with the light. || sample_name: LL4 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k !5 � 3W�DRS019579DRS019579OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time38 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL38 shows 38 hours later with the light. || sample_name: LL38 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10
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6H^p� � �k/ !5 � 3W�DRS019594DRS019594OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time64 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL64 shows 64 hours later with the light. || sample_name: LL64 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k. !5 � 3W�DRS019593DRS019593OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time62 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL62 shows 62 hours later with the light. || sample_name: LL62 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k- !5 � 3W�DRS019592DRS019592OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time60 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL60 shows 60 hours later with the light. || sample_name: LL60 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�g, !5 � 3W�DRS019591DRS019591OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time6 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL6 shows 6 hours later with the light. || sample_name: LL6 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k+ !5 � 3W�DRS019590DRS019590OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time58 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL58 shows 58 hours later with the light. || sample_name: LL58 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k* !5 � 3W�DRS019589DRS019589OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time56 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL56 shows 56 hours later with the light. || sample_name: LL56 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k) !5 � 3W�DRS019588DRS019588OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time54 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL54 shows 54 hours later with the light. || sample_name: LL54 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k( !5 � 3W�DRS019587DRS019587OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time52 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL52 shows 52 hours later with the light. || sample_name: LL52 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10
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6L �+4� %o- � �9 3 �\E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationaryERS016115ArrayExpressGenomics Core Facility, EMBL, Heidelberg, Germany2Escherichia coliProtocols: The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).Organism: Escherichia coli || StrainOrLine: K-12 substr. MG1655 || Genotype: wide_typeERA0141842016-11-20 05:31:37�g3 !5 � 3W�DRS019598DRS019598OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time8 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL8 shows 8 hours later with the light. || sample_name: LL8 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k2 !5 � 3W�DRS019597DRS019597OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time70 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL70 shows 70 hours later with the light. || sample_name: LL70 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k1 !5 � 3W�DRS019596DRS019596OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time68 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL68 shows 68 hours later with the light. || sample_name: LL68 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10�k0 !5 � 3W�DRS019595DRS019595OSAKA_PREF�Solanum lycopersicumsample_title: LL tomato Time66 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL64 shows 64 hours later with the light. || sample_name: LL66 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsuDRA0035282016-11-20 05:22:10
� �� �L6; %C/ �' �k 3 ��E-MTAB-552:Mature TuberERS023593ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber || DevelopmentalStage: mature || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06�#5} %o- � �9 3 �]E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Early_exponentialERS016116ArrayExpressGenomics Core Facility, EMBL, Heidelberg, Germany2Escherichia coliProtocols: The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).Organism: Escherichia coli || StrainOrLine: K-12 substr. MG1655 || Genotype: wide_typeERA0141842016-11-20 05:31:37
� � �57; %C/ �' �= 3 ��E-MTAB-552:Tuber sproutERS023594ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber sprout || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �J89 %C/ �' �i 3 ��E-MTAB-552:Young TuberERS023595ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber || DevelopmentalStage: young || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �197 %C/ �' �9 3 �E-MTAB-552:Tuber pithERS023596ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber pith || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �%:+ %C/ �' �- 3 �E-MTAB-552:LeafERS023597ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: leaf || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �);/ %C/ �' �1 3 �E-MTAB-552:StamenERS023598ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stamen || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �)</ %C/ �' �1 3 �E-MTAB-552:FlowerERS023599ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: flower || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �)=/ %C/ �' �1 3 �E-MTAB-552:StolonERS023600ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stolon || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �+>1 %C/ �' �3 3 �E-MTAB-552:PetioleERS023601ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: petiole || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �5?; %C/ �' �= 3 �E-MTAB-552:Tuber cortexERS023602ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber cortex || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �%@+ %C/ �' �- 3 �E-MTAB-552:RootERS023603ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: root || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �4AI %C/ �' �- 3 �E-MTAB-552:Water stressed leafERS023604ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: leaf || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �1B7 %C/ �' �9 3 �E-MTAB-552:Tuber peelERS023605ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber peel || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �1C7 %C/ �' �9 3 �E-MTAB-552:Shoot apexERS023606ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: shoot apex || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� � �%D+ %C/ �' �- 3 � E-MTAB-552:StemERS023607ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stem || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� �� �!FY %+/ �W �_ 3 WE-MTAB-861:Central starchy endosperm 4ERS074999ArrayExpressGATC BIOTECH AG�Triticum aestivumProtocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 21 d || OrganismPart: starchy endospermERA0708432016-11-20 05:51:46�<EK %C/ �' �; 3 �E-MTAB-552:Whole in vitro plantERS023608ArrayExpressAalborg University, DenmarkSolanum tuberosumProtocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: whole plant || BioSourceType: fresh_sampleERA0215692016-11-20 05:37:06
� ��� �!IY %+/ �W �_ 3 ZE-MTAB-861:Central starchy endosperm 1ERS075002ArrayExpressGATC BIOTECH AG�Triticum aestivumProtocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 10 d || OrganismPart: starchy endospermERA0708432016-11-20 05:51:46�!HY %+/ �W �_ 3 YE-MTAB-861:Central starchy endosperm 5ERS075001ArrayExpressGATC BIOTECH AG�Triticum aestivumProtocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 28 d || OrganismPart: starchy endospermERA0708432016-11-20 05:51:46�!GY %+/ �W �_ 3 XE-MTAB-861:Central starchy endosperm 2ERS075000ArrayExpressGATC BIOTECH AG�Triticum aestivumProtocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 14 d || OrganismPart: starchy endospermERA0708432016-11-20 05:51:46
� �� �aK1 % % �) �M 3C�E-MTAB-1585:7sk_3aERS225445ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18�!JY %+/ �W �_ 3 [E-MTAB-861:Central starchy endosperm 3ERS075003ArrayExpressGATC BIOTECH AG�Triticum aestivumProtocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 17 d || OrganismPart: starchy endospermERA0708432016-11-20 05:51:46
� �� �aM1 % % �) �M 3C�E-MTAB-1585:7sk_5aERS225447ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18�QL1 % % � �M 3C�E-MTAB-1585:7sk_1cERS225446ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18
� � �QO1 % % � �M 3C�E-MTAB-1585:7sk_4aERS225449ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18�aN1 % % �) �M 3C�E-MTAB-1585:7sk_6aERS225448ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18
� �� �aQ1 % % �) �M 3C�E-MTAB-1585:7sk_5cERS225451ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18�QP1 % % � �M 3C�E-MTAB-1585:7sk_4cERS225450ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18
� � �QS1 % % � �M 3C�E-MTAB-1585:7sk_1aERS225453ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18�aR1 % % �) �M 3C�E-MTAB-1585:7sk_2cERS225452ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18
8 8 �aU1 % % �) �M 3C�E-MTAB-1585:7sk_3cERS225455ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18�aT1 % % �) �M 3C�E-MTAB-1585:7sk_6cERS225454ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18
� � �QW1 % % � �M 3C�E-MTAB-1585:7sk_1bERS225457ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18�aV1 % % �) �M 3C�E-MTAB-1585:7sk_2aERS225456ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18
V �)*C V �j]1 % � 3 ��PRJNA39289.M980928SRS003454BI%�Homo sapiensn/an/an/aSample name: M980928 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�d\+ % � 3 ��PRJNA39289.MEWOSRS003453BI%�Homo sapiensn/an/an/aSample name: MEWO || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�|[ �_ �/ � 3 �~20527SRS000017WUGSC3@Streptococcus infantarius subsp. infantarius ATCC BAA-102Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriabioproject: 20527finishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.baSRA0002462016-11-20 10:07:54}Z9 9 ' 3 �yTachyglossus aculeatusSRS000290WUGSC$-Tachyglossus aculeatusnone providedSRA0002412016-11-20 10:07:54rY/ %% 3b"sample_AIG_104782ERS235800Genoscope�NAdineta vagaAdineta vagaERA2069992016-11-20 06:39:17�aX1 % % �) �M 3C�E-MTAB-1585:7sk_2bERS225458ArrayExpressEMBL-EBI'jMus musculusProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normalERA2037992016-11-20 06:37:18
9 &
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r ����YPI@ 9 �l ! % K �- 3,�14710B-4SRS2456864%�Homo sapiensbioproject: 399772: PRJNA399772isolate: treat2 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: HumanSRA6023132017-08-24 20:05:21�k ! % K �1 3,�14710B-1SRS2456863%�Homo sapiensbioproject: 399772: PRJNA399772isolate: control1 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: HumanSRA6023132017-08-24 20:05:21�j ! % K �- 3,�14710B-3SRS2456862%�Homo sapiensbioproject: 399772: PRJNA399772isolate: treat1 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: HumanSRA6023132017-08-24 20:05:21�i ! % K �1 3,�14710B-2SRS2456861%�Homo sapiensbioproject: 399772: PRJNA399772isolate: control2 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: HumanSRA6023132017-08-24 20:05:21�hhE ?3 �M 3 ��double-haploid rainbow troutSRS004650West Virginia University, VOncorhynchus mykissTissues were collected from a single immature (~ 1-year-old) male double-haploid fish and frozen in liquid nitrogen and stored at -80C until total RNA isolation. Total RNA was isolated using TRIzol™ (Invitrogen, Carlsbad, CA) from fourteen tissues; white muscle, red muscle, testis, spleen, kidney, head kidney, pituitary, stomach, brain, heart, intestine, gill, skin, liver. Equal masses of total RNAs from various tissues were pooled and used to construct the 454 library.SRA0092762016-11-20 10:09:03�gg1 % � 3 ��PRJNA39289.K-562-3SRS003464BI%�Homo sapiensn/an/an/aSample name: K-562-3 || geographic location (country and/or sea,region): missing || isolation source: K-562 || strain: missingSRA0090532016-11-20 10:08:56�gf1 % � 3 ��PRJNA39289.K-562-4SRS003463BI%�Homo sapiensn/an/an/aSample name: K-562-4 || geographic location (country and/or sea,region): missing || isolation source: K-562 || strain: missingSRA0090532016-11-20 10:08:56�je1 % � 3 ��PRJNA39289.M000921SRS003462BI%�Homo sapiensn/an/an/aSample name: M000921 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�jd1 % � 3 ��PRJNA39289.501 MELSRS003461BI%�Homo sapiensn/an/an/aSample name: 501 MEL || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�jc1 % � 3 ��PRJNA39289.M010403SRS003460BI%�Homo sapiensn/an/an/aSample name: M010403 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�jb1 % � 3 ��PRJNA39289.M970109SRS003459BI%�Homo sapiensn/an/an/aSample name: M970109 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�ja1 % � 3 ��PRJNA39289.M980409SRS003458BI%�Homo sapiensn/an/an/aSample name: M980409 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�j`1 % � 3 ��PRJNA39289.M990802SRS003457BI%�Homo sapiensn/an/an/aSample name: M990802 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�j_1 % � 3 ��PRJNA39289.M000216SRS003456BI%�Homo sapiensn/an/an/aSample name: M000216 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56�j^1 % � 3 ��PRJNA39289.M990514SRS003455BI%�Homo sapiensn/an/an/aSample name: M990514 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingSRA0090532016-11-20 10:08:56
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�� � �~{! 1 K � 3,��RNA21SRS2484901��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 900265.001 || cultivar: Karawa || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�z! e K � 3,��RNA16SRS2484900Z�Artocarpus altilis x Artocarpus mariannensisbioproject: 311339: PRJNA311339isolate: 890183.001 || cultivar: Midolab || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�y! e K � 3,��RNA48SRS2484899Z�Artocarpus altilis x Artocarpus mariannensisbioproject: 311339: PRJNA311339isolate: 890184.001 || cultivar: Luthar || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�{x! 1 K � 3,��RNA35SRS2484898
ѯArtocarpus camansibioproject: 311339: PRJNA311339isolate: 389.001 || cultivar: Kapiak || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�w! 1 K �' 3,��EW4SRS2484897
ѯArtocarpus camansibioproject: 311339: PRJNA311339isolate: 501 || cultivar: Kapiak || dev_stage: Seedling || geo_loc_name: USA: Hawaii || tissue: Root, Stem, and Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�yv! 1 K � 3,��EW2SRS2484896
ѯArtocarpus camansibioproject: 311339: PRJNA311339isolate: 501.005 || cultivar: Kapiak || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�u! ; K � 3,��RNA7SRS2484895
ѼArtocarpus mariannensisbioproject: 311339: PRJNA311339isolate: 900252.002 || cultivar: Dugdug || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56� t! 1 K � 3,��RNA34SRS2484894
ѯArtocarpus camansibioproject: 311339: PRJNA311339isolate: 890455.001 || cultivar: Ulu fatu || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�~s! 1 K � 3,��RNA5SRS2484893
ѯArtocarpus camansibioproject: 311339: PRJNA311339isolate: 770444.001 || cultivar: Camansi || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�r! 1 K � 3,��RNA37SRS2484892
ѯArtocarpus camansibioproject: 311339: PRJNA311339isolate: 980212.001 || cultivar: Camansi || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�~q! 1 K � 3,��RNA2SRS2484891
ѯArtocarpus camansibioproject: 311339: PRJNA311339isolate: 910280.001 || cultivar: Meikole || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�wp! 1 K � 3,��RNA38SRS2484890��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 880690.001 || cultivar: Kea || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�{o! 1 K � 3,��EW3SRS2484889��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 30042.001 || cultivar: Toneno || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�zn! 1 K � 3,��RNA39SRS2484888��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 790485.001 || cultivar: Puupuu || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�zm! 1 K � 3,��RNA49SRS2484887��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 910265.001 || cultivar: Rotuma || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56
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� �y{|�$p �0�! % K � 3,�A4SRS2484928%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 49 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: HumanSRA6047562017-09-07 19:59:56� �! % K �q 3,�A5SRS2484927%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 64 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: HumanSRA6047562017-09-07 19:59:56�0�! % K � 3,�A6SRS2484926%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 46 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: HumanSRA6047562017-09-07 19:59:56�{�! 1 K � 3,�RNA26SRS2484910��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 890167.002 || cultivar: Meisaip || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�z�! 1 K � 3,� RNA25SRS2484909��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 890479.002 || cultivar: Meisei || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56��! e K � 3,��RNA17SRS2484908Z�Artocarpus altilis x Artocarpus mariannensisbioproject: 311339: PRJNA311339isolate: 790487.001 || cultivar: Unk (Huehue) || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56��! e K � 3,��RNA40SRS2484907Z�Artocarpus altilis x Artocarpus mariannensisbioproject: 311339: PRJNA311339isolate: 910269.001 || cultivar: Faine || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56� � ! e K �' 3,��RNA36SRS2484906Z�Artocarpus altilis x Artocarpus mariannensisbioproject: 311339: PRJNA311339isolate: 890173.002 || cultivar: Ulu afa elise || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�! e K � 3,��RNA32SRS2484905Z�Artocarpus altilis x Artocarpus mariannensisbioproject: 311339: PRJNA311339isolate: 890174.001 || cultivar: Ulu afa || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�z~! 1 K � 3,��EW1SRS2484904��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 970236 || cultivar: Ulu fiti || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�}! e K � 3,��RNA10SRS2484903Z�Artocarpus altilis x Artocarpus mariannensisbioproject: 311339: PRJNA311339isolate: 790490.001 || cultivar: Rotuma || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56�||! 1 K � 3,��RNA24SRS2484902��Artocarpus altilisbioproject: 311339: PRJNA311339isolate: 900261.001 || cultivar: Samoan 2 || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: PlantSRA6047522017-09-07 19:59:56
E \ � P��P�E �c�!! % K �g 3-��GSM2791399SRS2534921%�Homo sapiensbioproject: 411985: PRJNA411985source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveSRA6125722017-10-05 20:45:55� �! % K �q 3,�D3SRS2484936%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 45 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: HumanSRA6047562017-09-07 19:59:56� �! % K �q 3,�D4SRS2484935%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 62 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: HumanSRA6047562017-09-07 19:59:56�4�
! % K � 3,�D2SRS2484934%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 72 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead not by breast cancer || BioSampleModel: HumanSRA6047562017-09-07 19:59:56� � ! % K �q 3,�D1SRS2484933%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 66 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: HumanSRA6047562017-09-07 19:59:56�0� ! % K � 3,�A2SRS2484932%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 60 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: HumanSRA6047562017-09-07 19:59:56�0�
! % K � 3,�A3SRS2484931%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 53 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: HumanSRA6047562017-09-07 19:59:56� � ! % K �q 3,�D5SRS2484930%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 69 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: HumanSRA6047562017-09-07 19:59:56� �! % K �q 3,�A1SRS2484929%�Homo sapiensbioproject: 399503: PRJNA399503isolate: breast cancer patient from Sweden || age: 40 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: HumanSRA6047562017-09-07 19:59:56
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� !! % K �5 3-�GSM2791568SRS2535697%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Total mRNA || barcode: O105 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57�� !! % K �I 3-�GSM2791566SRS2535696%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: O103 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57�
�!! % K �; 3-�GSM2791565SRS2535695%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: O102 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��!! % K �= 3-�GSM2791564SRS2535694%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O101 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��!! % K �? 3-�GSM2791563SRS2535693%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: O100 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��!! % K �A 3-�GSM2791562SRS2535692%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: O099 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57� �!! % K �3 3-�GSM2791561SRS2535691%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Total mRNA || barcode: O098 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57�
�!! % K �5 3-�GSM2791560SRS2535690%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Total mRNA || barcode: O097 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57�b�!! % K �e 3-��GSM2791404SRS2534926%�Homo sapiensbioproject: 411985: PRJNA411985source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveSRA6125722017-10-05 20:45:55�b�!! % K �e 3-��GSM2791402SRS2534925%�Homo sapiensbioproject: 411985: PRJNA411985source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveSRA6125722017-10-05 20:45:55�b�!! % K �e 3-��GSM2791403SRS2534924%�Homo sapiensbioproject: 411985: PRJNA411985source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveSRA6125722017-10-05 20:45:55�c�!! % K �g 3-��GSM2791401SRS2534923%�Homo sapiensbioproject: 411985: PRJNA411985source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveSRA6125722017-10-05 20:45:55�c�!! % K �g 3-��GSM2791400SRS2534922%�Homo sapiensbioproject: 411985: PRJNA411985source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveSRA6125722017-10-05 20:45:55
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� �zcQ@(� � ��+!! % K �C 3-�#GSM2791581SRS2535711%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: U779 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��*!! % K �E 3-�"GSM2791580SRS2535710%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Polysomal mRNA || barcode: U778 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��)!! % K �G 3-�!GSM2791579SRS2535709%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: U777 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��(!! % K �I 3-� GSM2791578SRS2535708%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: U776 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57�
�'!! % K �; 3-� GSM2791577SRS2535707%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Total mRNA || barcode: U775 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��&!! % K �= 3-� GSM2791576SRS2535706%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Total mRNA || barcode: U774 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��%!! % K �G 3-� GSM2791575SRS2535705%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: O112 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��$!! % K �I 3-� GSM2791574SRS2535704%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: O111 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57�
�#!! % K �; 3-�GSM2791573SRS2535703%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: O110 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��"!! % K �= 3-�GSM2791572SRS2535702%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O109 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��!!! % K �? 3-�GSM2791571SRS2535701%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: O108 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57� � !! % K �3 3-�GSM2791569SRS2535700%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Total mRNA || barcode: O106 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57�� !! % K �A 3-�GSM2791570SRS2535699%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: O107 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57�� !! % K �G 3-�GSM2791567SRS2535698%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: O104 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57
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� waL0��� � ��9 ! % � 3.K�Pat4024NSRS2554652%�Homo sapiensisolate: Prospective_4024_ID19_Norm || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��8 ! % � 3.K�Pat4024MSRS2554651%�Homo sapiensisolate: Prospective_4024_ID19_Met || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �7 ! % �! 3.K�Pat4024CSRS2554650%�Homo sapiensisolate: Prospective_4024_ID19_PrimTum || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��6 ! % � 3.K�Pat4037NSRS2554649%�Homo sapiensisolate: Prospective_4037_ID7_Norm || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��5!! % K �O 3-�-GSM2791591SRS2535721%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: U789 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��4!! % K �Q 3-�,GSM2791590SRS2535720%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: U788 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��3!! % K �C 3-�+GSM2791589SRS2535719%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: U787 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��2!! % K �E 3-�*GSM2791588SRS2535718%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Polysomal mRNA || barcode: U786 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��1!! % K �G 3-�)GSM2791587SRS2535717%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: U785 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��0!! % K �I 3-�(GSM2791586SRS2535716%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: U784 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57�
�/!! % K �; 3-�'GSM2791585SRS2535715%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Total mRNA || barcode: U783 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��.!! % K �= 3-�&GSM2791584SRS2535714%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Total mRNA || barcode: U782 || replicate: Biological replicate 2SRA6126182017-10-05 20:45:57��-!! % K �O 3-�%GSM2791583SRS2535713%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: U781 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57��,!! % K �Q 3-�$GSM2791582SRS2535712%�Homo sapiensbioproject: 412005: PRJNA412005source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: U780 || replicate: Biological replicate 1SRA6126182017-10-05 20:45:57
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q P@0 ��� � ��G! % � 3.L Pat235CSRS2554666%�Homo sapiensisolate: TEX_235_PrimTum || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07�
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Pat235MSRS2554665%�Homo sapiensisolate: TEX_235_Met || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Skin || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��E! % � 3.L Pat170CSRS2554664%�Homo sapiensisolate: TEX_170_PrimTum || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �D! % �{ 3.LPat170MSRS2554663%�Homo sapiensisolate: TEX_170_Met || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �C! % �} 3.LPat067NSRS2554662%�Homo sapiensisolate: TEX_067_Norm || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��B! % � 3.LPat224MSRS2554661%�Homo sapiensisolate: TEX_224_Met || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lymph node || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �A! % �} 3.LPat224NSRS2554660%�Homo sapiensisolate: TEX_224_Norm || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �@! % �} 3.LPat170NSRS2554659%�Homo sapiensisolate: TEX_179_Norm || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �?! % � 3.LPat224CSRS2554658%�Homo sapiensisolate: TEX_224_PrimTum || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast (lymph node) || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��> ! % � 3.LPat4005NSRS2554657%�Homo sapiensisolate: Prospective_4005_ID8_Norm || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��= ! % � 3.LPat4005MSRS2554656%�Homo sapiensisolate: Prospective_4005_ID8_Met || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �< ! % � 3.L Pat4005CSRS2554655%�Homo sapiensisolate: Prospective_4005_ID8_PrimTum || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �;! % �} 3.K�Pat235NSRS2554654%�Homo sapiensisolate: TEX_235_Norm || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �: ! % � 3.K�Pat4037CSRS2554653%�Homo sapiensisolate: Prospective_4037_ID7_PrimTum || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07
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�S! % �y 3.LPat067MSRS2554678%�Homo sapiensisolate: TEX_067_Met || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lung || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��R ! % � 3.LPat4037MSRS2554677%�Homo sapiensisolate: Prospective_4037_ID7_Met || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Bone || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �Q! % �} 3.LPat066NSRS2554676%�Homo sapiensisolate: TEX_066_Norm || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��P! % � 3.LPat067CSRS2554675%�Homo sapiensisolate: TEX_067_PrimTum || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �O! % �} 3.LPat044NSRS2554674%�Homo sapiensisolate: TEX_044_Norm || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �N! % � 3.LPat059CSRS2554673%�Homo sapiensisolate: TEX_059_PrimTum || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast (lymph node) || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��M! % � 3.LPat044CSRS2554672%�Homo sapiensisolate: TEX_044_PrimTum || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �L! % �{ 3.LPat044MSRS2554671%�Homo sapiensisolate: TEX_044_Met || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��K! % � 3.LPat066CSRS2554670%�Homo sapiensisolate: TEX_066_PrimTum || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �J! % �{ 3.LPat066MSRS2554669%�Homo sapiensisolate: TEX_066_Met || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: HumanSRA6157162017-10-19 20:02:07��I! % � 3.L
Pat059MSRS2554668%�Homo sapiensisolate: TEX_059_Met || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lymph node || BioSampleModel: HumanSRA6157162017-10-19 20:02:07� �H! % �} 3.L Pat059NSRS2554667%�Homo sapiensisolate: TEX_059_Norm || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: HumanSRA6157162017-10-19 20:02:07
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! 30P�SRS2707038SRA6329562017-11-30 17:55:17�J� !! ? K � 3."�GSM2806925SRS2575352mStreptomyces clavuligerusbioproject: 413703: PRJNA413703source_name: mycelium || phenotype: industrial strain || strain: F613-1SRA6179162017-10-12 20:17:05� � !! U K � 3."�GSM2806924SRS2575351�wStreptomyces clavuligerus ATCC 27064bioproject: 413703: PRJNA413703source_name: mycelium || phenotype: wildtype || strain: ATCC 27064 || type-material: type strain of Streptomyces clavuligerusSRA6179162017-10-12 20:17:05�2�
!! % K � 3."�GSM2806884SRS2575314'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�2� !! % K � 3."�GSM2806883SRS2575313'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�2�!! % K � 3."�GSM2806882SRS2575312'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�2�!! % K � 3."�GSM2806881SRS2575311'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�2�!! % K � 3."�GSM2806880SRS2575310'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�2�!! % K � 3."�GSM2806879SRS2575309'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�2�!! % K � 3."�GSM2806878SRS2575308'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�2�!! % K � 3."�GSM2806877SRS2575307'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�2�!! % K � 3."�GSM2806876SRS2575306'jMus musculusbioproject: 413695: PRJNA413695source_name: Liver || strain: C57BL/6 || genotype: wild typeSRA6179122017-10-12 20:17:05�F�!! % K �- 3.!�GSM2806690SRS2574064'jMus musculusbioproject: 413658: PRJNA413658source_name: helper T cell_CD3/28+cGAMP_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 3hrsSRA6178872017-10-12 20:17:03�H� !! % K �1 3.!�GSM2806695SRS2574063'jMus musculusbioproject: 413658: PRJNA413658source_name: helper T cell_CD3/28+cGAMP_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 24hrsSRA6178872017-10-12 20:17:03 � ?�������ugYK=/!���������yk]OA3%
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, a ;)I �Q )M 3P�DRX022400DRX022400KYOTO_SCIllumina MiSeq paired end sequencing of ABDRP002820DRP002820DRS021958DRS021958MiSeq_Anterior-blastemaRNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 338; �READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 126ILLUMINAIllumina MiSeqINSTRUMENT_MODEL: Illumina MiSeqDRA0027222016-11-19 08:06:05�S , a )I �O 3W 3�DRX005530DRX005530NIVTSTranscriptional sequence of 'F' pseudostemDRP002494DRP002494DRS005669DRS005669Shi_stemRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; �READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0009452016-11-19 08:02:28
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]|��9� 7 �~, !i )- �) 3W 3dEDRX030880DRX030880OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029600DRP002638DRP002638DRS019580DRS019580LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~, !i )- �) 3W 3dDDRX030879DRX030879OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029589DRP002638DRP002638DRS019569DRS019569LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~, !i )- �) 3W 3dCDRX030878DRX030878OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029583DRP002638DRP002638DRS019563DRS019563LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�^, )I �Q 3W 3] DRX026518DRX026518MIYAZAKIIllumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002611DRP002611DRS019416DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; �READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0029972017-04-20 18:52:34�^, )I �Q 3W 3] DRX026517DRX026517MIYAZAKIIllumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002610DRP002610DRS019416DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; �READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0029962017-06-22 18:51:11�^, )I �Q 3W 3]
DRX026516DRX026516MIYAZAKIIllumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002610DRP002610DRS019416DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; �READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0029962017-06-22 18:51:11�^, )I �Q 3W 3]DRX026509DRX026509MIYAZAKIIllumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRP002612DRS019417DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; �READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0029922016-11-19 08:06:38�^, )I �Q 3W 3]DRX026508DRX026508MIYAZAKIIllumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRP002612DRS019417DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; �READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0029922016-11-19 08:06:38�^, )I �Q 3W 3]DRX026507DRX026507MIYAZAKIIllumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRP002612DRS019417DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; �READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0029922016-11-19 08:06:38
� � } �{�y�w � �~%, !i )- �) 3W 3dODRX030890DRX030890OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029592DRP002638DRP002638DRS019572DRS019572LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~$, !i )- �) 3W 3dNDRX030889DRX030889OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029591DRP002638DRP002638DRS019571DRS019571LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~#, !i )- �) 3W 3dMDRX030888DRX030888OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029590DRP002638DRP002638DRS019570DRS019570LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~", !i )- �) 3W 3dLDRX030887DRX030887OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029588DRP002638DRP002638DRS019568DRS019568LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~!, !i )- �) 3W 3dKDRX030886DRX030886OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029587DRP002638DRP002638DRS019567DRS019567LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~ , !i )- �) 3W 3dJDRX030885DRX030885OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029586DRP002638DRP002638DRS019566DRS019566LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~ , !i )- �) 3W 3dIDRX030884DRX030884OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029585DRP002638DRP002638DRS019565DRS019565LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~ , !i )- �) 3W 3dHDRX030883DRX030883OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029584DRP002638DRP002638DRS019564DRS019564LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~ , !i )- �) 3W 3dGDRX030882DRX030882OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029618DRP002638DRP002638DRS019598DRS019598LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~ , !i )- �) 3W 3dFDRX030881DRX030881OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029611DRP002638DRP002638DRS019591DRS019591LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11
� � } �{�y�w � �~/, !i )- �) 3W 3dYDRX030900DRX030900OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029603DRP002638DRP002638DRS019583DRS019583LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~., !i )- �) 3W 3dXDRX030899DRX030899OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029602DRP002638DRP002638DRS019582DRS019582LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~-, !i )- �) 3W 3dWDRX030898DRX030898OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029601DRP002638DRP002638DRS019581DRS019581LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~,, !i )- �) 3W 3dVDRX030897DRX030897OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029599DRP002638DRP002638DRS019579DRS019579LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~+, !i )- �) 3W 3dUDRX030896DRX030896OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029598DRP002638DRP002638DRS019578DRS019578LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~*, !i )- �) 3W 3dTDRX030895DRX030895OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029597DRP002638DRP002638DRS019577DRS019577LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~), !i )- �) 3W 3dSDRX030894DRX030894OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029596DRP002638DRP002638DRS019576DRS019576LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~(, !i )- �) 3W 3dRDRX030893DRX030893OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029595DRP002638DRP002638DRS019575DRS019575LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~', !i )- �) 3W 3dQDRX030892DRX030892OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029594DRP002638DRP002638DRS019574DRS019574LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~&, !i )- �) 3W 3dPDRX030891DRX030891OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029593DRP002638DRP002638DRS019573DRS019573LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11
� � } �{�y�w � �~9, !i )- �) 3W 3dcDRX030910DRX030910OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029614DRP002638DRP002638DRS019594DRS019594LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~8, !i )- �) 3W 3dbDRX030909DRX030909OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029613DRP002638DRP002638DRS019593DRS019593LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~7, !i )- �) 3W 3daDRX030908DRX030908OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029612DRP002638DRP002638DRS019592DRS019592LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~6, !i )- �) 3W 3d`DRX030907DRX030907OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029610DRP002638DRP002638DRS019590DRS019590LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~5, !i )- �) 3W 3d_DRX030906DRX030906OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029609DRP002638DRP002638DRS019589DRS019589LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~4, !i )- �) 3W 3d^DRX030905DRX030905OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029608DRP002638DRP002638DRS019588DRS019588LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~3, !i )- �) 3W 3d]DRX030904DRX030904OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029607DRP002638DRP002638DRS019587DRS019587LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~2, !i )- �) 3W 3d\DRX030903DRX030903OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029606DRP002638DRP002638DRS019586DRS019586LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~1, !i )- �) 3W 3d[DRX030902DRX030902OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029605DRP002638DRP002638DRS019585DRS019585LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~0, !i )- �) 3W 3dZDRX030901DRX030901OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029604DRP002638DRP002638DRS019584DRS019584LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11
� } �d=/ S %+G! G� = � �) Cg �m 3 �IE-MTAB-387:Transition_to_StationaryERX007969ArrayExpressEMBL_HeidelbergRNA sequencing in E. coli K12E-MTAB-387ERP000350RNA sequencing in E. coli K12E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationaryERS016115Transition_to_StationaryOTHEROTHERcDNASINGLE - The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: GENOTYPE: wide_type || Experimental Factor: GROWTHCONDITION: transition-to-stationary-phaseERA0141842016-11-19 08:11:12�~<, !i )- �) 3W 3dfDRX030913DRX030913OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029617DRP002638DRP002638DRS019597DRS019597LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~;, !i )- �) 3W 3deDRX030912DRX030912OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029616DRP002638DRP002638DRS019596DRS019596LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11�~:, !i )- �) 3W 3ddDRX030911DRX030911OSAKA_PREFIllumina HiSeq 2000 sequencing of SAMD00029615DRP002638DRP002638DRS019595DRS019595LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - 3READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000DRA0035282016-11-19 08:07:11
� � �A>. E %+G! G} / � �) Cg �S 3 �JE-MTAB-387:Early_ExponentialERX007970ArrayExpressEMBL_HeidelbergRNA sequencing in E. coli K12E-MTAB-387ERP000350RNA sequencing in E. coli K12E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Early_exponentialERS016116Early_ExponentialOTHEROTHERcDNASINGLE - The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: GENOTYPE: wide_type || Experimental Factor: GROWTHCONDITION: early-exponentialERA0141842016-11-19 08:11:12
c c �?0 - % �M! �; ) � �) =a �C 3 �3E-MTAB-552:RHs08ERX010637ArrayExpressIllumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Mature TuberERS023593S8WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: tuber || Experimental Factor: DEVELOPMENTALSTAGE: matureERA0215692016-11-19 08:11:57
� � �w@/ - % �S! �; ) � �) Cg k 3 �4E-MTAB-552:RHs15ERX010638ArrayExpressIllumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Tuber sproutERS023594S15WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber sproutERA0215692016-11-19 08:11:57
e e �A0 - % �M! �9 ) � �) =a �A 3 �5E-MTAB-552:RHs07ERX010639ArrayExpressIllumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Young TuberERS023595S7WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: tuber || Experimental Factor: DEVELOPMENTALSTAGE: youngERA0215692016-11-19 08:11:57
� � �sB/ - % �S! �7 ) � �) Cg g 3 �6E-MTAB-552:RHs12ERX010640ArrayExpressIllumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Tuber pithERS023596S12WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber pithERA0215692016-11-19 08:11:57
� � �]C/ - % �M! �+ ) � �) =a [ 3 �7E-MTAB-552:RHs02ERX010641ArrayExpressIllumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:LeafERS023597S2WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: leafERA0215692016-11-19 08:11:57
� � �kD/ - % �S! �/ ) � �) Cg _ 3 �8E-MTAB-552:RHs10ERX010642ArrayExpressIllumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:StamenERS023598S10WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: stamenERA0215692016-11-19 08:11:57
� � �aE/ - % �M! �/ ) � �) =a _ 3 �9E-MTAB-552:RHs01ERX010643ArrayExpressIllumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:FlowerERS023599S1WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: flowerERA0215692016-11-19 08:11:57
� � �aF/ - % �M! �/ ) � �) =a _ 3 �:E-MTAB-552:RHs06ERX010644ArrayExpressIllumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:StolonERS023600S6WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: stolonERA0215692016-11-19 08:11:57
� � �cG/ - % �M! �1 ) � �) =a a 3 �;E-MTAB-552:RHs03ERX010645ArrayExpressIllumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:PetioleERS023601S3WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: petioleERA0215692016-11-19 08:11:57
� � �wH/ - % �S! �; ) � �) Cg k 3 �<E-MTAB-552:RHs16ERX010646ArrayExpressIllumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Tuber cortexERS023602S16WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber cortexERA0215692016-11-19 08:11:57
� � �fI/ - % �S! �+ ) � �) Cg [ 3 �=E-MTAB-552:RHs09ERX010647ArrayExpressIllumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:RootERS023603S9WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: rootERA0215692016-11-19 08:11:57
N N �/J0 - % �S! �I ) � �) Cg �K 3 �>E-MTAB-552:RHs11ERX010648ArrayExpressIllumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Water stressed leafERS023604S11WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: leaf || Experimental Factor: GROWTHCONDITION: water stressedERA0215692016-11-19 08:11:57
� � �sK/ - % �S! �7 ) � �) Cg g 3 �?E-MTAB-552:RHs13ERX010649ArrayExpressIllumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Tuber peelERS023605S13WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber peelERA0215692016-11-19 08:11:57
� � �iL/ - % �M! �7 ) � �) =a g 3 �@E-MTAB-552:RHs04ERX010650ArrayExpressIllumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Shoot apexERS023606S4WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: shoot apexERA0215692016-11-19 08:11:57
� � �]M/ - % �M! �+ ) � �) =a [ 3 �AE-MTAB-552:RHs05ERX010651ArrayExpressIllumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:StemERS023607S5WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: stemERA0215692016-11-19 08:11:57
B LB �O- 1 %+K! KY ') �A �) Cg I 3 ��E-MTAB-861:assay 4ERX033523ArrayExpressGATC Biotech AGwheat starchy endosperm RNA-SeqE-MTAB-861ERP001030wheat starchy endosperm RNA-SeqE-MTAB-861:Central starchy endosperm 4ERS074999RNA Extract 4RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 21 dERA0708432016-11-19 08:14:30�1N0 - % �S! �K ) � �) Cg �M 3 �BE-MTAB-552:RHs14ERX010652ArrayExpressIllumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552:Whole in vitro plantERS023608S14WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.$READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: whole plant || Experimental Factor: GROWTHCONDITION: in vitroERA0215692016-11-19 08:11:57
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�� � �R- 1 %+K! KY ') �A �) Cg I 3 �E-MTAB-861:assay 1ERX033526ArrayExpressGATC Biotech AGwheat starchy endosperm RNA-SeqE-MTAB-861ERP001030wheat starchy endosperm RNA-SeqE-MTAB-861:Central starchy endosperm 1ERS075002RNA Extract 1RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 10 dERA0708432016-11-19 08:14:31�Q- 1 %+K! KY ') �A �) Cg I 3 �E-MTAB-861:assay 5ERX033525ArrayExpressGATC Biotech AGwheat starchy endosperm RNA-SeqE-MTAB-861ERP001030wheat starchy endosperm RNA-SeqE-MTAB-861:Central starchy endosperm 5ERS075001RNA Extract 5RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 28 dERA0708432016-11-19 08:14:31�P- 1 %+K! KY ') �A �) Cg I 3 �E-MTAB-861:assay 2ERX033524ArrayExpressGATC Biotech AGwheat starchy endosperm RNA-SeqE-MTAB-861ERP001030wheat starchy endosperm RNA-SeqE-MTAB-861:Central starchy endosperm 2ERS075000RNA Extract 2RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 14 dERA0708432016-11-19 08:14:30
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�fT/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_3aERX221944ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_3aERS2254457sk_3aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)ERA2037992016-11-19 08:27:00�S- 1 %+K! KY ') �A �) Cg I 3 �E-MTAB-861:assay 3ERX033527ArrayExpressGATC Biotech AGwheat starchy endosperm RNA-SeqE-MTAB-861ERP001030wheat starchy endosperm RNA-SeqE-MTAB-861:Central starchy endosperm 3ERS075003RNA Extract 3RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 17 dERA0708432016-11-19 08:14:31
� � � �fV/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_5aERX221946ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_5aERS2254477sk_5aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)ERA2037992016-11-19 08:27:00�GU. 1 % � # � 1 ) �s 3W k 3F�E-MTAB-1585:7sk_1cERX221945ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_1cERS2254467sk_1cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneERA2037992016-11-19 08:27:00
� � �GX. 1 % � # � 1 ) �s 3W k 3F�E-MTAB-1585:7sk_4aERX221948ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_4aERS2254497sk_4aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneERA2037992016-11-19 08:27:00�fW/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_6aERX221947ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_6aERS2254487sk_6aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)ERA2037992016-11-19 08:27:00
� � � �fZ/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_5cERX221950ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_5cERS2254517sk_5cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)ERA2037992016-11-19 08:27:00�GY. 1 % � # � 1 ) �s 3W k 3F�E-MTAB-1585:7sk_4cERX221949ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_4cERS2254507sk_4cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneERA2037992016-11-19 08:27:00
� � �G\. 1 % � # � 1 ) �s 3W k 3F�E-MTAB-1585:7sk_1aERX221952ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_1aERS2254537sk_1aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneERA2037992016-11-19 08:27:00�f[/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_2cERX221951ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_2cERS2254527sk_2cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)ERA2037992016-11-19 08:27:00
. . �f^/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_3cERX221954ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_3cERS2254557sk_3cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)ERA2037992016-11-19 08:27:00�f]/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_6cERX221953ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_6cERS2254547sk_6cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)ERA2037992016-11-19 08:27:00
� � �G`. 1 % � # � 1 ) �s 3W k 3F�E-MTAB-1585:7sk_1bERX221956ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_1bERS2254577sk_1bRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneERA2037992016-11-19 08:27:00�f_/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_2aERX221955ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_2aERS2254567sk_2aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)ERA2037992016-11-19 08:27:00
� �� � �e- ! �9 O; !) �I!E = 3�Z2036533341SRX000121WUGSC454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831SRP000098 none provided Tachyglossus aculeatus SRS0002902036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241SRA0002412016-11-19 10:37:45�Nd, E E / ) ' �I3W 3j�exp_2.GAC.AIG_AOTS_GWDJGJ102ERX234950GSCAdineta vaga Titanium Simplestudy_AIGERP002474sample_AIG_104782ERS235800AIGAOTSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none provided �READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX TitaniumERA2069992016-11-19 08:28:11�Nc, E E / ) ' �I3W 3j�exp_1.GAC.AIG_AOTS_GWDJGJ101ERX234949GSCAdineta vaga Titanium Simplestudy_AIGERP002474sample_AIG_104782ERS235800AIGAOTSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none provided �READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX TitaniumERA2069992016-11-19 08:28:11�jb, = A / ) ' �) #G 3j�exp_AIG_AOSS_7_42RALAAXXERX234948GSCAdineta vaga GA IIx Simplestudy_AIGERP002474sample_AIG_104782ERS235800AIGAOSSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none providedLREAD_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAunspecifiedINSTRUMENT_MODEL: unspecifiedERA2069992016-11-19 08:28:11�fa/ 1 % � # � 1 ) � 3W � 3F�E-MTAB-1585:7sk_2bERX221957ArrayExpressEMBL-EBITranscriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585:7sk_2bERS2254587sk_2bRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)ERA2037992016-11-19 08:27:00
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� ��fF � j. 3 �g #)I �# Cg �E 3�30BV1AAXX080828-3-PSRX006124BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7010' containing sample 'M990514'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003455Solexa-7010RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26770.0 || lsid: BROAD:SEQUENCING_SAMPLE:26770.0 || material_type: New Tech Library || project: G1681 || work_request: 17302SRA0090532016-11-19 10:39:16� i. 3 �g #)I �# Cg �E 3�30BV1AAXX080828-2-PSRX006123BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7011' containing sample 'M980928'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003454Solexa-7011RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26771.0 || lsid: BROAD:SEQUENCING_SAMPLE:26771.0 || material_type: New Tech Library || project: G1681 || work_request: 17302SRA0090532016-11-19 10:39:16�h. 3 �a #)I �# Cg �E 3�30BV1AAXX080828-1-PSRX006122BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003453Solexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17302SRA0090532016-11-19 10:39:16�Bg- ! �U! O ! �I!E = 3�a2140631529SRX000023WUGSC454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333SRP000017 none provided Streptococcus infantarius subsp. infantarius ATCC BAA-102SRS0000172140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246SRA0002462016-11-19 10:37:45�f- ! �9 O; !) �I!E = 3�[2036546523SRX000122WUGSC454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831SRP000098 none provided Tachyglossus aculeatus SRS0002902036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241SRA0002412016-11-19 10:37:45
c � ��� c �o. 3 �a #)I �# Cg �E 3�30C3WAAXX080918-1-PSRX006129BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003453Solexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17462SRA0090532016-11-19 10:39:16� n. 3 �g #)I �# Cg �E 3�30BV1AAXX080828-8-PSRX006128BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7006' containing sample 'M970109'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003459Solexa-7006RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26766.0 || lsid: BROAD:SEQUENCING_SAMPLE:26766.0 || material_type: New Tech Library || project: G1681 || work_request: 17302SRA0090532016-11-19 10:39:16� m. 3 �g #)I �# Cg �E 3�30BV1AAXX080828-7-PSRX006127BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7007' containing sample 'M980409'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003458Solexa-7007RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26767.0 || lsid: BROAD:SEQUENCING_SAMPLE:26767.0 || material_type: New Tech Library || project: G1681 || work_request: 17302SRA0090532016-11-19 10:39:16� l. 3 �g #)I �# Cg �E 3�30BV1AAXX080828-6-PSRX006126BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7008' containing sample 'M990802'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003457Solexa-7008RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26768.0 || lsid: BROAD:SEQUENCING_SAMPLE:26768.0 || material_type: New Tech Library || project: G1681 || work_request: 17302SRA0090532016-11-19 10:39:16� k. 3 �g #)I �# Cg �E 3�30BV1AAXX080828-5-PSRX006125BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7009' containing sample 'M000216'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003456Solexa-7009RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26769.0 || lsid: BROAD:SEQUENCING_SAMPLE:26769.0 || material_type: New Tech Library || project: G1681 || work_request: 17302SRA0090532016-11-19 10:39:16
c � ��� c � t. 3 �g #)I �# Cg �E 3�30C3WAAXX080918-7-PSRX006134BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7015' containing sample 'K-562-4'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003463Solexa-7015RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26775.0 || lsid: BROAD:SEQUENCING_SAMPLE:26775.0 || material_type: New Tech Library || project: G1681 || work_request: 17461SRA0090532016-11-19 10:39:16� s. 3 �g #)I �# Cg �E 3�30C3WAAXX080918-6-PSRX006133BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7014' containing sample 'M000921'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003462Solexa-7014RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26774.0 || lsid: BROAD:SEQUENCING_SAMPLE:26774.0 || material_type: New Tech Library || project: G1681 || work_request: 17461SRA0090532016-11-19 10:39:16� r. 3 �g #)I �# Cg �E 3�30C3WAAXX080918-5-PSRX006132BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7013' containing sample '501 MEL'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003461Solexa-7013RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26773.0 || lsid: BROAD:SEQUENCING_SAMPLE:26773.0 || material_type: New Tech Library || project: G1681 || work_request: 17461SRA0090532016-11-19 10:39:16� q. 3 �g #)I �# Cg �E 3�30C3WAAXX080918-3-PSRX006131BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7005' containing sample 'M010403'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003460Solexa-7005RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26765.0 || lsid: BROAD:SEQUENCING_SAMPLE:26765.0 || material_type: New Tech Library || project: G1681 || work_request: 17461SRA0090532016-11-19 10:39:16�p. 3 �a #)I �# Cg �E 3�30C3WAAXX080918-2-PSRX006130BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003453Solexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17462SRA0090532016-11-19 10:39:16
� � � u. 3 �g #)I �# Cg �E 3�30C3WAAXX080918-8-PSRX006135BIIllumina whole genome shotgun sequencing of null paired-end library 'Solexa-7016' containing sample 'K-562-3'SRP000931Illumina sequencing of Homo sapiens via complementary DNASRS003464Solexa-7016RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 350; fREAD_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26776.0 || lsid: BROAD:SEQUENCING_SAMPLE:26776.0 || material_type: New Tech Library || project: G1681 || work_request: 17461SRA0090532016-11-19 10:39:16
�qv/ �5 ?�Q �+ ) �I!E 3%�Rainbow trout transcriptome analysis using Sanger and 454-Pyrosequencing approachesSRX007396West Virginia University,Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesSRP001007Messenger RNA was isolated from total RNA using the Oligotex mRNA Mini kit (Qiagen, CA). First and second strand cDNA were synthesized from 200ng of mRNA using the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen, CA) with 100 µM random hexamer primers (Fermentas, USA). Double-stranded cDNA was cleaned up with a QIAquick Minelute PCR purification column (Qiagen, CA). Double-stranded DNA was nebulized with the nebulization kit supplied with the GS Titanium Library Preparation kit (Roche/454 Life Sciences, CT) following their recommendations (30psi for 1 minute) and cleaned up with a QIAquick PCR minelute column and eluted in 50ul EB. Nebulized cDNA was blunt-ended (25 µl water, 10 µl 10x T4 DNA Ligase buffer (NEB), 4 µl 10 mM dNTP mix, 5 µl T4 DNA polymerase (3 U/µl) (NEB), 1 µl Klenow polymerase (5 U/ µl) (NEB), and 5 µl Polynucleotide kinase (10 U/µl) (NEB) and cleaned up with a Qiaquick PCR minelute column and eluted in 32ul EB. A dA-overhang was added at 3’ end of cDNA by adding the following to the blunt-ended cDNA: 5 µl 10x buffer 2 (NEB), 10 µl 1 mM dATP and 3 µl Klenow exo-minus polymerase (5 U/µl) (NEB). The reaction was incubated at 370C for 30 minutes and then cleaned up with a QIAquick MiniElute column and eluted in 10 µl EB. The cDNA was adaptored with Titanium adaptors (Roche/454 Life Sciences, CT) by adding 9 µl water, 25 µl 2x Rapid Ligase buffer (Enzymatics, MA) 5 µl (50 µM) Titanium adapter A/B mix and 1 µl T4 DNA Ligase (600 U/µl (Enzymatics, MA) and incubated the ligation reaction at room temperature for 15 minutes. The reaction was cleaned up using a Qiaquick MiniElute column (Qiagen), eluting the cDNA in 20 µl EB. Adaptored cDNA was run on a E-GEL EX 2% agarose (Invitrogen, CA) following the manufacturer instructions and cDNAs in the size range of 400-800bp were excised from the gel and purified with a Qiagen’s Gel Extraction kit and the cDNA was eluted in 30 µl EB. One µl of the gel- purified cDNA was used as template for amplification in 50 µl PCR reactions containing 10 µl 5x Phusion Buffer HF (NEB), 25 µM Adapter A_For primer (5’CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGT3’), 25 µM Adapter B_For primer (5’CCTATCCCCTGTGTGCCTTGGCAGTCTCAGT3’), 3% DMSO, 10 mM dNTPs and 1 U Phusion polymerase (Finnzymes/NEB, USA). The PCR conditions were as follows: 980C for 30 seconds, followed by 15 cycles with 980C for 10 seconds, 680C for 30 seconds and 720C for 30 seconds, with a final extension of 720C for 5 minute and cleaned up with a Qiaquick minelute PCR column. Normalization of cDNA library The cDNA library was normalized according to the protocol described in the Trimmer Direct Kit (Evrogen, Russia). In brief, 300 ng of cDNA were incubated at 950C for 5 minutes followed by incubation at 680C for 4 hours in the hybridization buffer included in the kit (50 mM Hepes, pH7.5 and 0.5 M NaCl). After the incubation, the reaction was treated with ¼ units of duplex specific nuclease (DSN). The normalized cDNA was then amplified from 1 µl of DSN-treated cDNA by PCR reactions (10 cycles) described above and gel purified for the fragment size of 400-800 bp as described above.SRS004650454ESTTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXSRA0092762016-11-19 10:39:43
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, ! Q � ! ) 3W 31��RNA24SRX3153048RNA-Seq of Artocarpus altilis leafSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484902RNA24RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55�}� , ! Y � ! ) 3W 31��RNA21SRX3153047RNA-Seq of Artocarpus altilis perianthSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484901RNA21RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55��- ! � � ! ) 3W 31��RNA16SRX3153046RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484900RNA16RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55��- ! � � ! ) 3W 31��RNA48SRX3153045RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484899RNA48RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55�}�, ! Y � ! ) 3W 31��RNA35SRX3153044RNA-Seq of Artocarpus camansi perianthSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484898RNA35RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55��, ! q � ! ) 3W 31��EW4SRX3153043RNA-Seq of Artocarpus camansi root, stem, and leafSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484897EW4RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55�y�, ! Y � ! ) 3W 31��EW2SRX3153042RNA-Seq of Artocarpus camansi perianthSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484896EW2RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55� �, ! c � ! ) 3W 31��RNA7SRX3153041RNA-Seq of Artocarpus mariannensis perianthSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484895RNA7RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55�}�, ! Y � ! ) 3W 31��RNA34SRX3153040RNA-Seq of Artocarpus camansi perianthSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484894RNA34RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55
� � � K ��!� � �G�, ! / �{ ! - #G 31�A5SRX3153077aneuploid tumor 5SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484927A5WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�G�, ! / �{ ! - #G 31� A6SRX3153076aneuploid tumor 6SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484926A6WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�y�, ! Q � ! ) 3W 31��RNA26SRX3153056RNA-Seq of Artocarpus altilis leafSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484910RNA26RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55�y�, ! Q � ! ) 3W 31��RNA25SRX3153055RNA-Seq of Artocarpus altilis leafSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484909RNA25RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55��- ! � � ! ) 3W 31��RNA17SRX3153054RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484908RNA17RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55��- ! � � ! ) 3W 31��RNA40SRX3153053RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafSRP116664Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingSRS2484907RNA40RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6047522017-09-07 19:18:55��- ! �
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� j !��B �E�, ! + �{ ! - #G 31�D2SRX3153083diploid tumor 2SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484934D2WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�G�, ! / �{ ! - #G 31�A2SRX3153082aneuploid tumor 2SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484932A2WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�G�, ! / �{ ! - #G 31�A3SRX3153081aneuploid tumor 3SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484931A3WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�E�, ! + �{ ! - #G 31�D5SRX3153080diploid tumor 5SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484930D5WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�G�, ! / �{ ! - #G 31�A1SRX3153079aneuploid tumor 1SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484929A1WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�G�, ! / �{ ! - #G 31�A4SRX3153078aneuploid tumor 4SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484928A4WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55
� n % � � - !! � ! ) �) 3W A 33�GSM2791400SRX3209940GSM2791400: HBCx-22 PDX treated with vehicle #2; Homo sapiens; RNA-SeqGSE104177SRP118776SRS2534922RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302791400: GSM2791400SRA6125722017-10-12 19:16:19� � - !! � ! ) �) 3W A 33�GSM2791399SRX3209939GSM2791399: HBCx-22 PDX treated with vehicle #1; Homo sapiens; RNA-SeqGSE104177SRP118776SRS2534921RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302791399: GSM2791399SRA6125722017-10-12 19:16:19�E� , ! + �{ ! - #G 31�
D3SRX3153086diploid tumor 3SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484936D3WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�E� , ! + �{ ! - #G 31� D4SRX3153085diploid tumor 4SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484935D4WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55�E�, ! + �{ ! - #G 31�D1SRX3153084diploid tumor 1SRP116668DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.SRS2484933D1WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500SRA6047562017-09-07 19:18:55
� � ��� � �#- !! � ! ) �) 3W A 33�GSM2791404SRX3209944GSM2791404: HBCx-22 PDX treated with RAD140 #6; Homo sapiens; RNA-SeqGSE104177SRP118776SRS2534926RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302791404: GSM2791404SRA6125722017-10-12 19:16:19� �"- !! � ! ) �) 3W A 33�GSM2791403SRX3209943GSM2791403: HBCx-22 PDX treated with RAD140 #5; Homo sapiens; RNA-SeqGSE104177SRP118776SRS2534924RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302791403: GSM2791403SRA6125722017-10-12 19:16:19� �!- !! � ! ) �) 3W A 33�GSM2791402SRX3209942GSM2791402: HBCx-22 PDX treated with RAD140 #4; Homo sapiens; RNA-SeqGSE104177SRP118776SRS2534925RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302791402: GSM2791402SRA6125722017-10-12 19:16:19� � - !! � ! ) �) 3W A 33� GSM2791401SRX3209941GSM2791401: HBCx-22 PDX treated with vehicle #3; Homo sapiens; RNA-SeqGSE104177SRP118776SRS2534923RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302791401: GSM2791401SRA6125722017-10-12 19:16:19
� N� �-�%, !! g ! ) �m 3W A ? 33�GSM2791561SRX3210844GSM2791561: 38HipTotal; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535691RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791561: GSM2791561GEO Accession: GSM2791561SRA6126182017-10-12 19:16:22�.�$, !! i ! ) �m 3W A ? 33�GSM2791560SRX3210843GSM2791560: 37NormTotal; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535690RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791560: GSM2791560GEO Accession: GSM2791560SRA6126182017-10-12 19:16:22
� L� �/�', !! k ! ) �m 3W A ? 33�GSM2791563SRX3210846GSM2791563: 40HipPPTotal; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535693RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791563: GSM2791563GEO Accession: GSM2791563SRA6126182017-10-12 19:16:22�0�&, !! m ! ) �m 3W A ? 33�GSM2791562SRX3210845GSM2791562: 39NormPPTotal; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535692RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791562: GSM2791562GEO Accession: GSM2791562SRA6126182017-10-12 19:16:22
� O� �,�), !! e ! ) �m 3W A ? 33� GSM2791565SRX3210848GSM2791565: 38HipPoly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535695RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791565: GSM2791565GEO Accession: GSM2791565SRA6126182017-10-12 19:16:22�-�(, !! g ! ) �m 3W A ? 33�GSM2791564SRX3210847GSM2791564: 37NormPoly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535694RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791564: GSM2791564GEO Accession: GSM2791564SRA6126182017-10-12 19:16:22
� M� �.�+, !! i ! ) �m 3W A ? 33� GSM2791567SRX3210850GSM2791567: 40HipPPPoly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535698RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791567: GSM2791567GEO Accession: GSM2791567SRA6126182017-10-12 19:16:22�/�*, !! k ! ) �m 3W A ? 33�
GSM2791566SRX3210849GSM2791566: 39NormPPPoly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535696RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791566: GSM2791566GEO Accession: GSM2791566SRA6126182017-10-12 19:16:22
� N� �-�-, !! g ! ) �m 3W A ? 33�
GSM2791569SRX3210852GSM2791569: 42HipTotal; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535700RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791569: GSM2791569GEO Accession: GSM2791569SRA6126182017-10-12 19:16:22�.�,, !! i ! ) �m 3W A ? 33� GSM2791568SRX3210851GSM2791568: 41NormTotal; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535697RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791568: GSM2791568GEO Accession: GSM2791568SRA6126182017-10-12 19:16:22
� L� �/�/, !! k ! ) �m 3W A ? 33�GSM2791571SRX3210854GSM2791571: 44HipPPTotal; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535701RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791571: GSM2791571GEO Accession: GSM2791571SRA6126182017-10-12 19:16:22�0�., !! m ! ) �m 3W A ? 33�GSM2791570SRX3210853GSM2791570: 43NormPPTotal; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535699RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791570: GSM2791570GEO Accession: GSM2791570SRA6126182017-10-12 19:16:22
� O� �,�1, !! e ! ) �m 3W A ? 33�GSM2791573SRX3210856GSM2791573: 42HipPoly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535703RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791573: GSM2791573GEO Accession: GSM2791573SRA6126182017-10-12 19:16:22�-�0, !! g ! ) �m 3W A ? 33�GSM2791572SRX3210855GSM2791572: 41NormPoly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535702RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791572: GSM2791572GEO Accession: GSM2791572SRA6126182017-10-12 19:16:22
� M� �.�3, !! i ! ) �m 3W A ? 33�GSM2791575SRX3210858GSM2791575: 44HipPPPoly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535705RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791575: GSM2791575GEO Accession: GSM2791575SRA6126182017-10-12 19:16:22�/�2, !! k ! ) �m 3W A ? 33�GSM2791574SRX3210857GSM2791574: 43NormPPPoly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535704RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791574: GSM2791574GEO Accession: GSM2791574SRA6126182017-10-12 19:16:22
� P� �,�5, !! e ! ) �m 3W A ? 33�GSM2791577SRX3210860GSM2791577: 66H_Total; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535707RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791577: GSM2791577GEO Accession: GSM2791577SRA6126182017-10-12 19:16:22�,�4, !! e ! ) �m 3W A ? 33�GSM2791576SRX3210859GSM2791576: 65N_Total; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535706RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791576: GSM2791576GEO Accession: GSM2791576SRA6126182017-10-12 19:16:22
� N� �.�7, !! i ! ) �m 3W A ? 33�GSM2791579SRX3210862GSM2791579: 68HPP_Total; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535709RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791579: GSM2791579GEO Accession: GSM2791579SRA6126182017-10-12 19:16:22�.�6, !! i ! ) �m 3W A ? 33�GSM2791578SRX3210861GSM2791578: 67NPP_Total; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535708RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791578: GSM2791578GEO Accession: GSM2791578SRA6126182017-10-12 19:16:22
� Q� �+�9, !! c ! ) �m 3W A ? 33�GSM2791581SRX3210864GSM2791581: 66H_Poly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535711RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791581: GSM2791581GEO Accession: GSM2791581SRA6126182017-10-12 19:16:22�+�8, !! c ! ) �m 3W A ? 33�GSM2791580SRX3210863GSM2791580: 65N_Poly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535710RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791580: GSM2791580GEO Accession: GSM2791580SRA6126182017-10-12 19:16:22
� O� �-�;, !! g ! ) �m 3W A ? 33�GSM2791583SRX3210866GSM2791583: 68HPP_Poly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535713RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791583: GSM2791583GEO Accession: GSM2791583SRA6126182017-10-12 19:16:22�-�:, !! g ! ) �m 3W A ? 33�GSM2791582SRX3210865GSM2791582: 67NPP_Poly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535712RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791582: GSM2791582GEO Accession: GSM2791582SRA6126182017-10-12 19:16:22
� P� �,�=, !! e ! ) �m 3W A ? 33� GSM2791585SRX3210868GSM2791585: 82H_Total; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535715RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791585: GSM2791585GEO Accession: GSM2791585SRA6126182017-10-12 19:16:22�,�<, !! e ! ) �m 3W A ? 33� GSM2791584SRX3210867GSM2791584: 81N_Total; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535714RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791584: GSM2791584GEO Accession: GSM2791584SRA6126182017-10-12 19:16:22
� N� �.�?, !! i ! ) �m 3W A ? 33� GSM2791587SRX3210870GSM2791587: 84HPP_Total; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535717RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791587: GSM2791587GEO Accession: GSM2791587SRA6126182017-10-12 19:16:22�.�>, !! i ! ) �m 3W A ? 33� GSM2791586SRX3210869GSM2791586: 83NPP_Total; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791586: GSM2791586GEO Accession: GSM2791586SRA6126182017-10-12 19:16:22
� Q� �+�A, !! c ! ) �m 3W A ? 33�!GSM2791589SRX3210872GSM2791589: 82H_Poly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535719RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791589: GSM2791589GEO Accession: GSM2791589SRA6126182017-10-12 19:16:22�+�@, !! c ! ) �m 3W A ? 33� GSM2791588SRX3210871GSM2791588: 81N_Poly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535718RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791588: GSM2791588GEO Accession: GSM2791588SRA6126182017-10-12 19:16:22
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��D- ! � �{ ! - 3W 33�]Pat4037MSRX3230136Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554677Pat4037MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31�-�C, !! g ! ) �m 3W A ? 33�#GSM2791591SRX3210874GSM2791591: 84HPP_Poly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535721RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791591: GSM2791591GEO Accession: GSM2791591SRA6126182017-10-12 19:16:22�-�B, !! g ! ) �m 3W A ? 33�"GSM2791590SRX3210873GSM2791590: 83NPP_Poly; Homo sapiens; RNA-SeqGSE104193SRP118788SRS2535720RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302791590: GSM2791590GEO Accession: GSM2791590SRA6126182017-10-12 19:16:22
< l � D � ��b� < ��N- ! � �{ ! - 3W 33�gPat224CSRX3230146Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554658Pat224COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��M- ! � �{ ! - 3W 33�fPat4005NSRX3230145Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554657Pat4005NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��L- ! � �{ ! - 3W 33�ePat4005MSRX3230144Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554656Pat4005MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��K- ! � �{ ! - 3W 33�dPat4005CSRX3230143Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554655Pat4005COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��J- ! � �{ ! - 3W 33�cPat235NSRX3230142Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554654Pat235NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��I- ! � �{ ! - 3W 33�bPat4037CSRX3230141Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554653Pat4037COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��H- ! � �{ ! - 3W 33�aPat4024NSRX3230140Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554652Pat4024NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��G- ! � �{ ! - 3W 33�`Pat4024MSRX3230139Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554651Pat4024MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��F- ! � �{ ! - 3W 33�_Pat4024CSRX3230138Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554650Pat4024COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��E- ! � �{ ! - 3W 33�^Pat4037NSRX3230137Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554649Pat4037NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31
L n � J �&�p� L ��X- ! � �{ ! - 3W 33�qPat059NSRX3230156Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554667Pat059NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��W- ! � �{ ! - 3W 33�pPat235CSRX3230155Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554666Pat235COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��V- ! � �{ ! - 3W 33�oPat235MSRX3230154Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554665Pat235MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��U- ! � �{ ! - 3W 33�nPat170CSRX3230153Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554664Pat170COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��T- ! � �{ ! - 3W 33�mPat170MSRX3230152Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554663Pat170MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��S- ! � �{ ! - 3W 33�lPat067MSRX3230151Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554678Pat067MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��R- ! � �{ ! - 3W 33�kPat067NSRX3230150Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554662Pat067NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��Q- ! � �{ ! - 3W 33�jPat224MSRX3230149Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554661Pat224MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��P- ! � �{ ! - 3W 33�iPat224NSRX3230148Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554660Pat224NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��O- ! � �{ ! - 3W 33�hPat170NSRX3230147Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554659Pat170NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31
� n � J �&�p� ��a- ! � �{ ! - 3W 33�zPat066NSRX3230165Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554676Pat066NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��`- ! � �{ ! - 3W 33�yPat067CSRX3230164Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554675Pat067COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��_- ! � �{ ! - 3W 33�xPat044NSRX3230163Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554674Pat044NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��^- ! � �{ ! - 3W 33�wPat059CSRX3230162Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554673Pat059COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��]- ! � �{ ! - 3W 33�vPat044CSRX3230161Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554672Pat044COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��\- ! � �{ ! - 3W 33�uPat044MSRX3230160Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554671Pat044MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��[- ! � �{ ! - 3W 33�tPat066CSRX3230159Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554670Pat066COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��Z- ! � �{ ! - 3W 33�sPat066MSRX3230158Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554669Pat066MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31��Y- ! � �{ ! - 3W 33�rPat059MSRX3230157Whole Exome Sequencing of breast cancer tumor and metastaseSRP119112Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)SRS2554668Pat059MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000SRA6157162017-10-19 19:08:31
}
?} �>�c- !! �A ! ) �1 3W A ? 33�"GSM2806528SRX3257823GSM2806528: K8 CLIP-seq-1 in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711SRP119540SRS2571284RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302806528: GSM2806528GEO Accession: GSM2806528SRA6177832017-10-12 19:21:55�=�b- !! �? ! ) �1 3W A ? 33�!GSM2806527SRX3257822GSM2806527: IgG CLIP-seq in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711SRP119540SRS2571283RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302806527: GSM2806527GEO Accession: GSM2806527SRA6177832017-10-12 19:21:55
�
>�� � �Y�g, !! k ! ) �A 3W A ? 33ϳGSM2806560SRX3259104GSM2806560: DEX_1hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572537RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806560: GSM2806560GEO Accession: GSM2806560SRA6178092017-10-12 19:21:59�Y�f, !! k ! ) �A 3W A ? 33ϲGSM2806559SRX3259103GSM2806559: DEX_1hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572536RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806559: GSM2806559GEO Accession: GSM2806559SRA6178092017-10-12 19:21:59�!�e- !! � ! ) �1 3W A ? 33�$GSM2806530SRX3257825GSM2806530: K8 CLIP-seq in BJAB cells; Homo sapiens; RIP-SeqGSE104711SRP119540SRS2571286RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeqâ„¢ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302806530: GSM2806530GEO Accession: GSM2806530SRA6177832017-10-12 19:21:55�>�d- !! �A ! ) �1 3W A ? 33�#GSM2806529SRX3257824GSM2806529: K8 CLIP-seq-2 in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711SRP119540SRS2571285RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeqâ„¢ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500gds: 302806529: GSM2806529GEO Accession: GSM2806529SRA6177832017-10-12 19:21:55
# F
i���� �Y�o, !! k ! ) �A 3W A ? 33ϻGSM2806568SRX3259112GSM2806568: DEX_9hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572545RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806568: GSM2806568GEO Accession: GSM2806568SRA6178092017-10-12 19:21:59�Y�n, !! k ! ) �A 3W A ? 33ϺGSM2806567SRX3259111GSM2806567: DEX_9hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572544RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806567: GSM2806567GEO Accession: GSM2806567SRA6178092017-10-12 19:21:59�Y�m, !! k ! ) �A 3W A ? 33ϹGSM2806566SRX3259110GSM2806566: DEX_7hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572543RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806566: GSM2806566GEO Accession: GSM2806566SRA6178092017-10-12 19:21:59�Y�l, !! k ! ) �A 3W A ? 33ϸGSM2806565SRX3259109GSM2806565: DEX_7hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572542RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806565: GSM2806565GEO Accession: GSM2806565SRA6178092017-10-12 19:21:59�Y�k, !! k ! ) �A 3W A ? 33ϷGSM2806564SRX3259108GSM2806564: DEX_5hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572541RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806564: GSM2806564GEO Accession: GSM2806564SRA6178092017-10-12 19:21:59�Y�j, !! k ! ) �A 3W A ? 33϶GSM2806563SRX3259107GSM2806563: DEX_5hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572540RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806563: GSM2806563GEO Accession: GSM2806563SRA6178092017-10-12 19:21:59�Y�i, !! k ! ) �A 3W A ? 33ϵGSM2806562SRX3259106GSM2806562: DEX_3hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572539RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806562: GSM2806562GEO Accession: GSM2806562SRA6178092017-10-12 19:21:59�Y�h, !! k ! ) �A 3W A ? 33ϴGSM2806561SRX3259105GSM2806561: DEX_3hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572538RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806561: GSM2806561GEO Accession: GSM2806561SRA6178092017-10-12 19:21:59
" D
f���� �Z�w, !! m ! ) �A 3W A ? 33��GSM2806576SRX3259120GSM2806576: EtOH_5hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572553RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806576: GSM2806576GEO Accession: GSM2806576SRA6178092017-10-12 19:21:59�Z�v, !! m ! ) �A 3W A ? 33��GSM2806575SRX3259119GSM2806575: EtOH_5hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572552RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806575: GSM2806575GEO Accession: GSM2806575SRA6178092017-10-12 19:21:59�Z�u, !! m ! ) �A 3W A ? 33�GSM2806574SRX3259118GSM2806574: EtOH_3hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572551RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806574: GSM2806574GEO Accession: GSM2806574SRA6178092017-10-12 19:21:59�Z�t, !! m ! ) �A 3W A ? 33�GSM2806573SRX3259117GSM2806573: EtOH_3hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572550RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806573: GSM2806573GEO Accession: GSM2806573SRA6178092017-10-12 19:21:59�Z�s, !! m ! ) �A 3W A ? 33ϿGSM2806572SRX3259116GSM2806572: EtOH_1hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572549RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806572: GSM2806572GEO Accession: GSM2806572SRA6178092017-10-12 19:21:59�Z�r, !! m ! ) �A 3W A ? 33ϾGSM2806571SRX3259115GSM2806571: EtOH_1hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572548RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806571: GSM2806571GEO Accession: GSM2806571SRA6178092017-10-12 19:21:59�Z�q, !! m ! ) �A 3W A ? 33ϽGSM2806570SRX3259114GSM2806570: DEX_11hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572547RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806570: GSM2806570GEO Accession: GSM2806570SRA6178092017-10-12 19:21:59�Z�p, !! m ! ) �A 3W A ? 33ϼGSM2806569SRX3259113GSM2806569: DEX_11hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572546RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806569: GSM2806569GEO Accession: GSM2806569SRA6178092017-10-12 19:21:59
c " D
f���c �c�~, !! ! ) �A 3W A ? 33�GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716SRP119575SRS2573343RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806589: GSM2806589GEO Accession: GSM2806589SRA6178422017-10-12 19:22:00�[�}, !! o ! ) �A 3W A ? 33��GSM2806582SRX3259126GSM2806582: EtOH_11hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572559RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806582: GSM2806582GEO Accession: GSM2806582SRA6178092017-10-12 19:21:59�[�|, !! o ! ) �A 3W A ? 33��GSM2806581SRX3259125GSM2806581: EtOH_11hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572558RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806581: GSM2806581GEO Accession: GSM2806581SRA6178092017-10-12 19:21:59�Z�{, !! m ! ) �A 3W A ? 33��GSM2806580SRX3259124GSM2806580: EtOH_9hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572557RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806580: GSM2806580GEO Accession: GSM2806580SRA6178092017-10-12 19:21:59�Z�z, !! m ! ) �A 3W A ? 33��GSM2806579SRX3259123GSM2806579: EtOH_9hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572556RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806579: GSM2806579GEO Accession: GSM2806579SRA6178092017-10-12 19:21:59�Z�y, !! m ! ) �A 3W A ? 33��GSM2806578SRX3259122GSM2806578: EtOH_7hr_Rep2; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572555RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806578: GSM2806578GEO Accession: GSM2806578SRA6178092017-10-12 19:21:59�Z�x, !! m ! ) �A 3W A ? 33��GSM2806577SRX3259121GSM2806577: EtOH_7hr_Rep1; Homo sapiens; RNA-SeqGSE104714SRP119557SRS2572554RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806577: GSM2806577GEO Accession: GSM2806577SRA6178092017-10-12 19:21:59
�
� 2�e�� �b�, !! } ! ) �A 3W A ? 33�GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716SRP119575SRS2573350RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806595: GSM2806595GEO Accession: GSM2806595SRA6178422017-10-12 19:22:00�b�, !! } ! ) �A 3W A ? 33�GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716SRP119575SRS2573348RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806594: GSM2806594GEO Accession: GSM2806594SRA6178422017-10-12 19:22:00�b�, !! } ! ) �A 3W A ? 33�GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716SRP119575SRS2573347RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806593: GSM2806593GEO Accession: GSM2806593SRA6178422017-10-12 19:22:00�c�, !! ! ) �A 3W A ? 33�GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716SRP119575SRS2573346RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806592: GSM2806592GEO Accession: GSM2806592SRA6178422017-10-12 19:22:00�c� , !! ! ) �A 3W A ? 33�GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716SRP119575SRS2573345RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806591: GSM2806591GEO Accession: GSM2806591SRA6178422017-10-12 19:22:00�c�, !! ! ) �A 3W A ? 33�GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716SRP119575SRS2573344RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806590: GSM2806590GEO Accession: GSM2806590SRA6178422017-10-12 19:22:00
�
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, !! u ! ) �; 3W A ? 33ОGSM2806690SRX3260748GSM2806690: CD3/28+cGAMP_3h_1; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574064RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806690: GSM2806690GEO Accession: GSM2806690SRA6178872017-10-12 19:22:02�U� , !! i ! ) �; 3W A ? 33НGSM2806689SRX3260747GSM2806689: CD3/28_3h_2; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574057RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806689: GSM2806689GEO Accession: GSM2806689SRA6178872017-10-12 19:22:02�U�, !! i ! ) �; 3W A ? 33МGSM2806688SRX3260746GSM2806688: CD3/28_3h_1; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574055RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806688: GSM2806688GEO Accession: GSM2806688SRA6178872017-10-12 19:22:02�U�, !! i ! ) �; 3W A ? 33ЛGSM2806687SRX3260745GSM2806687: Naive CD4_2; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574056RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806687: GSM2806687GEO Accession: GSM2806687SRA6178872017-10-12 19:22:02�U�, !! i ! ) �; 3W A ? 33КGSM2806686SRX3260744GSM2806686: Naive CD4_1; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574058RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806686: GSM2806686GEO Accession: GSM2806686SRA6178872017-10-12 19:22:02�b�, !! } ! ) �A 3W A ? 33�GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716SRP119575SRS2573349RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806596: GSM2806596GEO Accession: GSM2806596SRA6178422017-10-12 19:22:00
-
� G��- �\�, !! w ! ) �; 3W A ? 33УGSM2806695SRX3260753GSM2806695: CD3/28+cGAMP_24h_2; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574063RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806695: GSM2806695GEO Accession: GSM2806695SRA6178872017-10-12 19:22:02�\�, !! w ! ) �; 3W A ? 33ТGSM2806694SRX3260752GSM2806694: CD3/28+cGAMP_24h_1; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574062RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806694: GSM2806694GEO Accession: GSM2806694SRA6178872017-10-12 19:22:02�V�
, !! k ! ) �; 3W A ? 33СGSM2806693SRX3260751GSM2806693: CD3/28_24h_2; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574061RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806693: GSM2806693GEO Accession: GSM2806693SRA6178872017-10-12 19:22:02�V� , !! k ! ) �; 3W A ? 33РGSM2806692SRX3260750GSM2806692: CD3/28_24h_1; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574060RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806692: GSM2806692GEO Accession: GSM2806692SRA6178872017-10-12 19:22:02�[� , !! u ! ) �; 3W A ? 33ПGSM2806691SRX3260749GSM2806691: CD3/28+cGAMP_3h_2; Mus musculus; RNA-SeqGSE104725SRP119595SRS2574059RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500gds: 302806691: GSM2806691GEO Accession: GSM2806691SRA6178872017-10-12 19:22:02
� H�� �4�, !! { ! ) �g 3W A ? 33�_GSM2806878SRX3262380GSM2806878: Liver - Corn Oil KS3; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575308RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806878: GSM2806878GEO Accession: GSM2806878SRA6179122017-10-12 19:22:04�4�, !! { ! ) �g 3W A ? 33�^GSM2806877SRX3262379GSM2806877: Liver - Corn Oil KS2; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575307RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806877: GSM2806877GEO Accession: GSM2806877SRA6179122017-10-12 19:22:04�4�, !! { ! ) �g 3W A ? 33�]GSM2806876SRX3262378GSM2806876: Liver - Corn Oil KS1; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575306RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806876: GSM2806876GEO Accession: GSM2806876SRA6179122017-10-12 19:22:04
� M�� �/�, !! q ! ) �g 3W A ? 33�bGSM2806881SRX3262383GSM2806881: Liver - PCN KS6; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575311RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806881: GSM2806881GEO Accession: GSM2806881SRA6179122017-10-12 19:22:04�/�, !! q ! ) �g 3W A ? 33�aGSM2806880SRX3262382GSM2806880: Liver - PCN KS5; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575310RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806880: GSM2806880GEO Accession: GSM2806880SRA6179122017-10-12 19:22:04�/�, !! q ! ) �g 3W A ? 33�`GSM2806879SRX3262381GSM2806879: Liver - PCN KS4; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575309RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806879: GSM2806879GEO Accession: GSM2806879SRA6179122017-10-12 19:22:04
� J�� �2�, !! w ! ) �g 3W A ? 33�eGSM2806884SRX3262386GSM2806884: Liver - TCPOBOP K9; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575314RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806884: GSM2806884GEO Accession: GSM2806884SRA6179122017-10-12 19:22:04�2�, !! w ! ) �g 3W A ? 33�dGSM2806883SRX3262385GSM2806883: Liver - TCPOBOP K8; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575313RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806883: GSM2806883GEO Accession: GSM2806883SRA6179122017-10-12 19:22:04�2�, !! w ! ) �g 3W A ? 33�cGSM2806882SRX3262384GSM2806882: Liver - TCPOBOP K7; Mus musculus; RNA-SeqGSE104734SRP119609SRS2575312RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806882: GSM2806882GEO Accession: GSM2806882SRA6179122017-10-12 19:22:04
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SRX3323022SRA6242242017-11-16 17:53:30T�"+ ! 35^�SRX3322945SRA6241712017-11-16 17:53:30T�!+ ! 35^�SRX3322944SRA6241712017-11-16 17:53:30T� + ! 35^�SRX3322943SRA6241702017-11-16 17:53:30T� + ! 35^�SRX3322942SRA6241702017-11-16 17:53:30T� + ! 35^�SRX3322869SRA6241352017-11-16 17:53:30T� + ! 35^�SRX3322868SRA6241352017-11-16 17:53:30T� + ! 35^WSRX3322823SRA6241032017-11-16 17:53:30T�+ ! 35^VSRX3322822SRA6241032017-11-16 17:53:30�<�, !! y ! ) �y 3W A ? 33�gGSM2806925SRX3262428GSM2806925: F613-1; Streptomyces clavuligerus; RNA-SeqGSE104738SRP119613SRS2575352RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806925: GSM2806925GEO Accession: GSM2806925SRA6179162017-10-12 19:22:04�?�, !! ! ) �y 3W A ? 33�fGSM2806924SRX3262427GSM2806924: ATCC27064; Streptomyces clavuligerus; RNA-SeqGSE104738SRP119613SRS2575351RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000gds: 302806924: GSM2806924GEO Accession: GSM2806924SRA6179162017-10-12 19:22:04
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+ ! 3<G�SRX3741802SRA6621022018-03-08 17:52:48T� + ! 3<G�SRX3741801SRA6621022018-03-08 17:52:48T� + ! 3<G�SRX3741800SRA6621022018-03-08 17:52:48T�
+ ! 3<G�SRX3741799SRA6621022018-03-08 17:52:48T� + ! 3<G�SRX3741798SRA6621022018-03-08 17:52:48T�+ ! 3<G�SRX3741797SRA6621022018-03-08 17:52:48T�+ ! 3<G�SRX3741796SRA6621022018-03-08 17:52:48T�+ ! 3<G�SRX3741795SRA6621022018-03-08 17:52:48T�+ ! 3<G�SRX3741794SRA6621022018-03-08 17:52:48T�+ ! 3<G�SRX3741793SRA6621022018-03-08 17:52:48T�+ ! 3<G�SRX3741792SRA6621022018-03-08 17:52:48T�+ ! 3;�dSRX3722250SRA6603742018-03-01 17:53:11T�+ ! 3;�cSRX3722249SRA6603742018-03-01 17:53:11T� + ! 3;�bSRX3722248SRA6603742018-03-01 17:53:11T�+ ! 3;�aSRX3722247SRA6603742018-03-01 17:53:11T�~+ ! 3;�`SRX3722246SRA6603742018-03-01 17:53:11T�}+ ! 3;�_SRX3722245SRA6603742018-03-01 17:53:11T�|+ ! 3;�^SRX3722244SRA6603742018-03-01 17:53:11T�{+ ! 3;�]SRX3722243SRA6603742018-03-01 17:53:11T�z+ ! 3;.7SRX3683141SRA6587132018-02-22 17:53:47T�y+ ! 36�1SRX3413863SRA6329562017-12-07 17:52:32T�x+ ! 36�0SRX3413862SRA6329562017-12-07 17:52:32T�w+ ! 36�/SRX3413858SRA6329562017-12-07 17:52:32T�v+ ! 36�.SRX3413856SRA6329562017-12-07 17:52:32T�u+ ! 36]�SRX3413861SRA6329562017-11-30 17:52:55T�t+ ! 36]�SRX3413860SRA6329562017-11-30 17:52:55T�s+ ! 36]�SRX3413859SRA6329562017-11-30 17:52:55T�r+ ! 36]�SRX3413857SRA6329562017-11-30 17:52:55T�q+ ! 36]�SRX3413855SRA6329562017-11-30 17:52:55T�p+ ! 36Z4SRX3412321SRA6326512017-11-30 17:52:55T�o+ ! 36Z3SRX3412320SRA6326512017-11-30 17:52:55T�n+ ! 36Z2SRX3412319SRA6326512017-11-30 17:52:55T�m+ ! 36Z1SRX3412318SRA6326512017-11-30 17:52:55T�l+ ! 36Z0SRX3412317SRA6326512017-11-30 17:52:55T�k+ ! 36Z/SRX3412316SRA6326512017-11-30 17:52:55T�j+ ! 36Z.SRX3412315SRA6326512017-11-30 17:52:55
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+ ! 3<�SRX3758447SRA6639242018-03-22 17:52:02T� + ! 3<�SRX3758446SRA6639242018-03-22 17:52:02T� + ! 3<�SRX3758445SRA6639242018-03-22 17:52:02T�
+ ! 3<�SRX3758444SRA6639242018-03-22 17:52:02T� + ! 3<�SRX3758443SRA6639242018-03-22 17:52:02T�+ ! 3<�SRX3758442SRA6639242018-03-22 17:52:02T�+ ! 3<�SRX3758441SRA6639242018-03-22 17:52:02T�+ ! 3<�SRX3758440SRA6639242018-03-22 17:52:02T�+ ! 3<�SRX3758439SRA6639242018-03-22 17:52:02T�+ ! 3<�SRX3758438SRA6639242018-03-22 17:52:02T�+ ! 3<�SRX3758437SRA6639242018-03-22 17:52:02T�+ ! 3<�
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3 � q�E���W�+��i � �e E 3 E 3�hrun_1.GAC.AIG_AOTS_GWDJGJ101ERR2603772011-01-20 00:00:00GenoscopeERX234949exp_1.GAC.AIG_AOTS_GWDJGJ101ERA2069992016-11-19 17:51:18�d = 3 = 3�grun_AIG_AOSS_7_42RALAAXXERR2603762009-09-21 00:00:00GenoscopeERX234948exp_AIG_AOSS_7_42RALAAXXERA2069992016-11-19 17:51:18�c = % 9 1 3�E-MTAB-1585:7sk_2a.fq.gzERR247423ArrayExpressROCKEFELLER UNIVERSITYERX221955E-MTAB-1585:7sk_2aERA2037992016-11-19 17:50:10�b = % 9 1 3�E-MTAB-1585:7sk_5c.fq.gzERR247422ArrayExpressROCKEFELLER UNIVERSITYERX221950E-MTAB-1585:7sk_5cERA2037992016-11-19 17:50:10�a = % 9 1 3�E-MTAB-1585:7sk_6a.fq.gzERR247421ArrayExpressROCKEFELLER UNIVERSITYERX221947E-MTAB-1585:7sk_6aERA2037992016-11-19 17:50:10�` = % 9 1 3�E-MTAB-1585:7sk_3a.fq.gzERR247420ArrayExpressROCKEFELLER UNIVERSITYERX221944E-MTAB-1585:7sk_3aERA2037992016-11-19 17:50:10�_ = % 9 1 3�E-MTAB-1585:7sk_2b.fq.gzERR247419ArrayExpressROCKEFELLER UNIVERSITYERX221957E-MTAB-1585:7sk_2bERA2037992016-11-19 17:50:10�^ = % 9 1 3�E-MTAB-1585:7sk_3c.fq.gzERR247418ArrayExpressROCKEFELLER UNIVERSITYERX221954E-MTAB-1585:7sk_3cERA2037992016-11-19 17:50:10�] = % 9 1 3�
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E-MTAB-1585:7sk_5a.fq.gzERR247414ArrayExpressROCKEFELLER UNIVERSITYERX221946E-MTAB-1585:7sk_5aERA2037992016-11-19 17:50:10�Y = % 9 1 3� E-MTAB-1585:7sk_1c.fq.gzERR247413ArrayExpressROCKEFELLER UNIVERSITYERX221945E-MTAB-1585:7sk_1cERA2037992016-11-19 17:50:10�X = % 9 1 3�E-MTAB-1585:7sk_6c.fq.gzERR247412ArrayExpressROCKEFELLER UNIVERSITYERX221953E-MTAB-1585:7sk_6cERA2037992016-11-19 17:50:10�W = % 9 1 3�E-MTAB-1585:7sk_1a.fq.gzERR247411ArrayExpressROCKEFELLER UNIVERSITYERX221952E-MTAB-1585:7sk_1aERA2037992016-11-19 17:50:10�V = % 9 1 3�E-MTAB-1585:7sk_4a.fq.gzERR247410ArrayExpressROCKEFELLER UNIVERSITYERX221948E-MTAB-1585:7sk_4aERA2037992016-11-19 17:50:10�U A % + 1 3TvE-MTAB-861:28days.fastq.gzERR056481ArrayExpressGATC BIOTECH AGERX033525E-MTAB-861:assay 5ERA0708432016-11-19 17:38:28�T A % + 1 3TuE-MTAB-861:21days.fastq.gzERR056480ArrayExpressGATC BIOTECH AGERX033523E-MTAB-861:assay 4ERA0708432016-11-19 17:38:28�S A % + 1 3TtE-MTAB-861:17days.fastq.gzERR056479ArrayExpressGATC BIOTECH AGERX033527E-MTAB-861:assay 3ERA0708432016-11-19 17:38:28�R A % + 1 3TsE-MTAB-861:14days.fastq.gzERR056478ArrayExpressGATC BIOTECH AGERX033524E-MTAB-861:assay 2ERA0708432016-11-19 17:38:28�Q A % + 1 3TrE-MTAB-861:10days.fastq.gzERR056477ArrayExpressGATC BIOTECH AGERX033526E-MTAB-861:assay 1ERA0708432016-11-19 17:38:28�P ; % C - 3�E-MTAB-552:RHs16.txt.gzERR029924ArrayExpressAalborg University, DenmarkERX010646E-MTAB-552:RHs16ERA0215692016-11-19 17:35:32�O ; % C - 3�E-MTAB-552:RHs15.txt.gzERR029923ArrayExpressAalborg University, DenmarkERX010638E-MTAB-552:RHs15ERA0215692016-11-19 17:35:32�N ; % C - 3�E-MTAB-552:RHs14.txt.gzERR029922ArrayExpressAalborg University, DenmarkERX010652E-MTAB-552:RHs14ERA0215692016-11-19 17:35:32�M ; % C - 3�E-MTAB-552:RHs13.txt.gzERR029921ArrayExpressAalborg University, DenmarkERX010649E-MTAB-552:RHs13ERA0215692016-11-19 17:35:32�L ; % C - 3�E-MTAB-552:RHs12.txt.gzERR029920ArrayExpressAalborg University, DenmarkERX010640E-MTAB-552:RHs12ERA0215692016-11-19 17:35:32
F b
�T��F �Wl 3 ! �U 3w�EUEMSW401SRR0006522007-08-22 00:00:00WUGSCSRX0001212036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wk 3 ! �U 3w�EUEMSW404SRR0006512007-08-22 00:00:00WUGSCSRX0001212036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wj 3 ! �U 3w�EUEMSW407SRR0006502007-08-22 00:00:00WUGSCSRX0001222036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wi 3 ! �U 3w�EUGXWLM02SRR0006492007-08-23 00:00:00WUGSCSRX0001222036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wh 3 ! �U 3w�EUEMSW405SRR0006482007-08-22 00:00:00WUGSCSRX0001222036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wg 3 ! �U 3w�EUGXWLM01SRR0006472007-08-23 00:00:00WUGSCSRX0001212036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�f E 3 E 3�irun_2.GAC.AIG_AOTS_GWDJGJ102ERR2603782011-01-20 00:00:00GenoscopeERX234950exp_2.GAC.AIG_AOTS_GWDJGJ102ERA2069992016-11-19 17:51:18
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� L��>� �Wr 3 ! �U 3w�EUPZL4S02SRR0006582007-08-28 00:00:00WUGSCSRX0001222036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wq 3 ! �U 3w�EUEMSW406SRR0006572007-08-22 00:00:00WUGSCSRX0001222036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wp 3 ! �U 3w�EUPZL4S01SRR0006562007-08-28 00:00:00WUGSCSRX0001212036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wo 3 ! �U 3w�EUEMSW408SRR0006552007-08-22 00:00:00WUGSCSRX0001222036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wn 3 ! �U 3w�EUEMSW402SRR0006542007-08-22 00:00:00WUGSCSRX0001212036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28�Wm 3 ! �U 3w�EUEMSW403SRR0006532007-08-22 00:00:00WUGSCSRX0001212036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002412016-11-19 19:54:28
I
� L��>� I �y � �! 3�BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.1SRR018256BISRX006122analysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 1 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302SRA0090532016-11-19 20:03:15�Wx 3 ! �U 3w�EXRHO8E06SRR0001422007-10-23 00:00:00WUGSCSRX0000232140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002462016-11-19 19:54:29�Ww 3 ! �U 3w�EZNCMKS01SRR0001412007-11-28 00:00:00WUGSCSRX0000232140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002462016-11-19 19:54:29�Wv 3 ! �U 3w�EZNCMKS02SRR0001402007-11-28 00:00:00WUGSCSRX0000232140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002462016-11-19 19:54:29�Wu 3 ! �U 3w�EXRHO8E07SRR0001392007-10-23 00:00:00WUGSCSRX0000232140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002462016-11-19 19:54:29�Wt 3 ! �U 3w�EXRHO8E08SRR0001382007-10-23 00:00:00WUGSCSRX0000232140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002462016-11-19 19:54:29�Ws 3 ! �U 3w�EXRHO8E05SRR0001372007-10-23 00:00:00WUGSCSRX0000232140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGSRA0002462016-11-19 19:54:29
� e � / ��^�"� �� � �! 3��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.3SRR018265BISRX006131analysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26765.0 || instrument_name: SL-XAN || lane: 3 || lsid: BROAD:SEQUENCING_SAMPLE:26765.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461SRA0090532016-11-19 20:03:15�� � �! 3��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.2SRR018264BISRX006130analysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 2 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17462SRA0090532016-11-19 20:03:15�� � �! 3��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.1SRR018263BISRX006129analysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 1 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17462SRA0090532016-11-19 20:03:15� � �! 3��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.8SRR018262BISRX006128analysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26766.0 || instrument_name: SL-XAN || lane: 8 || lsid: BROAD:SEQUENCING_SAMPLE:26766.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302SRA0090532016-11-19 20:03:15�~ � �! 3��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.7SRR018261BISRX006127analysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26767.0 || instrument_name: SL-XAN || lane: 7 || lsid: BROAD:SEQUENCING_SAMPLE:26767.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302SRA0090532016-11-19 20:03:15�} � �! 3��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.6SRR018260BISRX006126analysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26768.0 || instrument_name: SL-XAN || lane: 6 || lsid: BROAD:SEQUENCING_SAMPLE:26768.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302SRA0090532016-11-19 20:03:15�| � �! 3��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.5SRR018259BISRX006125analysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26769.0 || instrument_name: SL-XAN || lane: 5 || lsid: BROAD:SEQUENCING_SAMPLE:26769.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302SRA0090532016-11-19 20:03:15�{ � �! 3��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.3SRR018258BISRX006124analysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26770.0 || instrument_name: SL-XAN || lane: 3 || lsid: BROAD:SEQUENCING_SAMPLE:26770.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302SRA0090532016-11-19 20:03:15�z � �! 3��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.2SRR018257BISRX006123analysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26771.0 || instrument_name: SL-XAN || lane: 2 || lsid: BROAD:SEQUENCING_SAMPLE:26771.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302SRA0090532016-11-19 20:03:15
p b � & � �B�b��8�~!�i �R��;��) � p Y� -! ! 38fRNA5_R2.fastq.gzSRR5997533SRX3153039SRA6047522017-09-07 19:37:38Z� /! ! 38eRNA34_R2.fastq.gzSRR5997532SRX3153040SRA6047522017-09-07 19:37:38Y� -! ! 38dRNA7_R1.fastq.gzSRR5997531SRX3153041SRA6047522017-09-07 19:37:38X� +! ! 38cEW2_R2.fastq.gzSRR5997530SRX3153042SRA6047522017-09-07 19:37:38X� +! ! 38bEW4_R1.fastq.gzSRR5997529SRX3153043SRA6047522017-09-07 19:37:38Z� /! ! 38aRNA35_R1.fastq.gzSRR5997528SRX3153044SRA6047522017-09-07 19:37:38Z� /! ! 38`RNA48_R1.fastq.gzSRR5997527SRX3153045SRA6047522017-09-07 19:37:38Z� /! ! 38_RNA16_R2.fastq.gzSRR5997526SRX3153046SRA6047522017-09-07 19:37:38Z� /! ! 38^RNA21_R2.fastq.gzSRR5997525SRX3153047SRA6047522017-09-07 19:37:38Z� /! ! 38]RNA24_R2.fastq.gzSRR5997524SRX3153048SRA6047522017-09-07 19:37:38Z� /! ! 38\RNA10_R2.fastq.gzSRR5997523SRX3153049SRA6047522017-09-07 19:37:38X� +! ! 38[EW1_R2.fastq.gzSRR5997522SRX3153050SRA6047522017-09-07 19:37:38Z� /! ! 38ZRNA32_R1.fastq.gzSRR5997521SRX3153051SRA6047522017-09-07 19:37:38Z� /! ! 38YRNA36_R2.fastq.gzSRR5997520SRX3153052SRA6047522017-09-07 19:37:38Z� /! ! 38XRNA40_R1.fastq.gzSRR5997519SRX3153053SRA6047522017-09-07 19:37:38Z� /! ! 38WRNA17_R1.fastq.gzSRR5997518SRX3153054SRA6047522017-09-07 19:37:38Z� /! ! 38VRNA25_R1.fastq.gzSRR5997517SRX3153055SRA6047522017-09-07 19:37:38Z�
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��{5��me J #kindexrun_acc_idxrun �CREATE INDEX run_acc_idx on run (run_accession)�
�wtablerunrun �CREATE TABLE `run` (
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`run_date` TEXT,
`run_file` TEXT,
`run_center` TEXT,
`total_data_blocks` INTEGER,
`experiment_accession` TEXT,
`experiment_name` TEXT,
`sra_link` TEXT,
`run_url_link` TEXT,
`xref_link` TEXT,
`run_entrez_link` TEXT,
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)n 1!�indexexperiment_acc_idxexperiment �CREATE INDEX experiment_acc_idx on experiment (experiment_accession)�C!!�Qtableexperimentexperiment@CREATE TABLE `experiment` (
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`fastqFTP` TEXT,
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`experiment_accession` TEXT,
`broker_name` TEXT,
`center_name` TEXT,
`title` TEXT,
`study_name` TEXT,
`study_accession` TEXT,
`design_description` TEXT,
`sample_name` TEXT,
`sample_accession` TEXT,
`sample_member` TEXT,
`library_name` TEXT,
`library_strategy` TEXT,
`library_source` TEXT,
`library_selection` TEXT,
`library_layout` TEXT,
`targeted_loci` TEXT,
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`spot_length` INTEGER,
`adapter_spec` TEXT,
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`platform` TEXT,
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`quality_scorer` TEXT,
`number_of_levels` INTEGER,
`multiplier` TEXT,
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`xref_link` TEXT,
`experiment_entrez_link` TEXT,
`ddbj_link` TEXT,
`ena_link` TEXT,
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)X)}indexsample_acc_idxsample=CREATE INDEX sample_acc_idx on sample (sample_accession)�
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`scientific_name` TEXT,
`common_name` TEXT,
`anonymized_name` TEXT,
`individual_name` TEXT,
`description` TEXT,
`sra_link` TEXT,
`sample_url_link` TEXT,
`xref_link` TEXT,
`sample_entrez_link` TEXT,
`ddbj_link` TEXT,
`ena_link` TEXT,
`sample_attribute` TEXT,
`submission_accession` TEXT,
`sradb_updated` TEXT
)S'windexstudy_acc_idxstudyCREATE INDEX study_acc_idx on study (study_accession)�!�!tablestudystudyCREATE TABLE `study` (
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`broker_name` TEXT,
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`files` TEXT,
`broker_name` TEXT,
`center_name` TEXT,
`lab_name` TEXT,
`submission_date` TEXT,
`sra_link` TEXT,
`submission_url_link` TEXT,
`xref_link` TEXT,
`submission_entrez_link` TEXT,
`ddbj_link` TEXT,
`ena_link` TEXT,
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`sradb_updated` TEXT
)X �tablemetaInfometaInfoCREATE TABLE metaInfo (name varchar(50), value varchar(50))
� X
8�XT T
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�Utablesra_ftsra_ftCREATE VIRTUAL TABLE sra_ft USING fts3 ( SRR_bamFile,SRX_bamFile,SRX_fastqFTP,run_ID,run_alias,run_accession,run_date,updated_date,spots,bases,run_center,experiment_name,run_url_link,run_entrez_link,run_attribute,experiment_ID,experiment_alias,experiment_accession,experiment_title,study_name,sample_name,design_description,library_name,library_strategy,library_source,library_selection,library_layout,library_construction_protocol,adapter_spec,read_spec,platform,instrument_model,instrument_name,platform_parameters,sequence_space,base_caller,quality_scorer,number_of_levels,multiplier,qtype,experiment_url_link,experiment_entrez_link,experiment_attribute,sample_ID,sample_alias,sample_accession,taxon_id,common_name,anonymized_name,individual_name,description,sample_url_link,sample_entrez_link,sample_attribute,study_ID,study_alias,study_accession,study_title,study_type,study_abstract,center_project_name,study_description,study_url_link,study_entrez_link,study_attribute,related_studies,primary_study,submission_ID,submission_accession,submission_comment,submission_center,submission_lab,submission_date,sradb_updated )�^ �!tablesrasra �CREATE TABLE `sra` (
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`SRR_bamFile` TEXT,
`SRX_bamFile` TEXT,
`SRX_fastqFTP` TEXT,
`run_ID` REAL,
`run_alias` TEXT,
`run_accession` TEXT,
`run_date` TEXT,
`updated_date` TEXT,
`spots` REAL,
`bases` REAL,
`run_center` TEXT,
`experiment_name` TEXT,
`run_url_link` TEXT,
`run_entrez_link` TEXT,
`run_attribute` TEXT,
`experiment_ID` REAL,
`experiment_alias` TEXT,
`experiment_accession` TEXT,
`experiment_title` TEXT,
`study_name` TEXT,
`sample_name` TEXT,
`design_description` TEXT,
`library_name` TEXT,
`library_strategy` TEXT,
`library_source` TEXT,
`library_selection` TEXT,
`library_layout` TEXT,
`library_construction_protocol` TEXT,
`adapter_spec` TEXT,
`read_spec` TEXT,
`platform` TEXT,
`instrument_model` TEXT,
`instrument_name` TEXT,
`platform_parameters` TEXT,
`sequence_space` TEXT,
`base_caller` TEXT,
`quality_scorer` TEXT,
`number_of_levels` INTEGER,
`multiplier` TEXT,
`qtype` TEXT,
`experiment_url_link` TEXT,
`experiment_entrez_link` TEXT,
`experiment_attribute` TEXT,
`sample_ID` REAL,
`sample_alias` TEXT,
`sample_accession` TEXT,
`taxon_id` INTEGER,
`common_name` TEXT,
`anonymized_name` TEXT,
`individual_name` TEXT,
`description` TEXT,
`sample_url_link` TEXT,
`sample_entrez_link` TEXT,
`sample_attribute` TEXT,
`study_ID` REAL,
`study_alias` TEXT,
`study_accession` TEXT,
`study_title` TEXT,
`study_type` TEXT,
`study_abstract` TEXT,
`center_project_name` TEXT,
`study_description` TEXT,
`study_url_link` TEXT,
`study_entrez_link` TEXT,
`study_attribute` TEXT,
`related_studies` TEXT,
`primary_study` TEXT,
`submission_ID` REAL,
`submission_accession` TEXT,
`submission_comment` TEXT,
`submission_center` TEXT,
`submission_lab` TEXT,
`submission_date` TEXT,
`sradb_updated` TEXT
)J #kindexrun_acc_idxrun �CREATE INDEX run_acc_idx on run (run_accession) |�wtablerunrun �CREATE TABLE `run` (
`run_ID` REAL,
`bamFile` TEXT,
`run_alias` TEXT,
`run_accession` TEXT,
`broker_name` TEXT,
`instrument_name` TEXT,
`run_date` TEXT,
`run_file` TEXT,
`run_center` TEXT,
`total_data_blocks` INTEGER,
`experiment_accession` TEXT,
`experiment_name` TEXT,
`sra_link` TEXT,
`run_url_link` TEXT,
`xref_link` TEXT,
`run_entrez_link` TEXT,
`ddbj_link` TEXT,
`ena_link` TEXT,
`run_attribute` TEXT,
`submission_accession` TEXT,
`sradb_updated` TEXT
)n 1!�indexexperiment_acc_idxexperiment �CREATE INDEX experiment_acc_idx on experiment (experiment_accession)
� � �yO !! a )I �O 3 W ) / a9�)/�) E 3��DRR006300DRR0063002012-03-212015-10-21 � � �qyNIVTSDRX005524�DRX005524DRX005524Transcriptional sequence of 'Aka' meristemDRP002494DRS005663Aka_meriRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 20009DRS005663DRS005663 �#bunching onionMeristem of 'Aka'aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11�wO !! ] )I �O 3 W ) - a9�)/�) E 3��DRR006304DRR0063042012-03-212015-10-21 �'� �@ NIVTSDRX005528�DRX005528DRX005528Transcriptional sequence of 'Ki' flowersDRP002494DRS005667Ki_flowerRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000=DRS005667DRS005667 �#bunching onionMeristem of 'Ki'aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11�vO !! Y )I �O 3 W ) 5 a9�)/�) E 3��DRR006299DRR0062992012-03-212015-10-21 �ʏ ��l�BGIDRX005523�DRX005523DRX005523Transcriptional sequence of 'Aka' leafDRP002494DRS005662Aka_leafRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 20008DRS005662DRS005662 �#bunching onionMature leaf of 'Aka'aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11�yO !! e )I �O 3 W ) + a9�)/�) E 3��DRR006303DRR0063032012-03-212015-10-21 �>� ��1HNIVTSDRX005527�DRX005527DRX005527Transcriptional sequence of 'Aka' pseudostemDRP002494DRS005666Aka_stemRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000<DRS005666DRS005666 �#bunching onionFlowers of 'Ki'aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11
J wB�J �rO !! Y )I �O 3 W ) ) a9�)/�) E 3��DRR006301DRR0063012012-03-212015-10-21 Ӵ �ڢHNIVTSDRX005525�DRX005525DRX005525Transcriptional sequence of 'Aka' rootDRP002494DRS005664Aka_rootRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000:DRS005664DRS005664 �#bunching onionRoots of 'Aka'aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11� O !! a )I �O 3 W ) = a9�)/�) E 3��DRR006306DRR0063062012-03-212015-10-21 �sr ��,(NIVTSDRX005530�DRX005530DRX005530Transcriptional sequence of 'F' pseudostemDRP002494DRS005669Shi_stemRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000?DRS005669DRS005669 �#bunching onionMature pseudostem of 'F'aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11�2P !! _ )I �M3 W ) �7 a9�)/�) E 3��DRR006298DRR0062982012-02-262015-02-04�q+���NIASDRX005522�DRX005522DRX005522Transcriptional sequence of 'Ki' from 454DRP002494DRS005661LIY01RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 450; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 1LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX Titanium7DRS005661DRS005661 �#bunching onionMixture of nine tissues from inbred 'Ki' (2-weeks seedlings, leaf, roots, basal meristem, immature flower bract, mature bract (about 1 week before anthesis), opened flowers, immature fruits and sliced pseudostem).aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11�O !! c %)I �O 3 W ) ? a9�)/�) E 3��DRR006302DRR0063022012-03-212015-10-21 ȼ| �$�0NIVTSDRX005526�DRX005526DRX005526Transcriptional sequence of 'Aka' seedlingsDRP002494DRS005665Aka_seedlingRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000;DRS005665DRS005665 �#bunching onion2-week seedlings of 'Aka'aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11
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DRR024742DRR0247422015-12-29��>qI�DRX022406P�DRX022406DRX022406454 GS FLX+ sequencing of PBDRP002820DRS021959454-P_Posterior-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX+INSTRUMENT_MODEL: 454 GS FLX+H5DRS021959DRS021959sex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�
Q ! E =) �)# G � u�A� �9 3\�[DRR024746DRR0247462015-12-29H ��DRX022406P�DRX022406DRX022406454 GS FLX+ sequencing of PBDRP002820DRS021959454-P_Posterior-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX+INSTRUMENT_MODEL: 454 GS FLX+H5DRS021959DRS021959sex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11� O !! a )I �O 3 W ) A a9�)/�) E 3��DRR006305DRR0063052012-03-212015-10-21 ӭ �յ�NIVTSDRX005529�DRX005529DRX005529Transcriptional sequence of 'Ki' meristemsDRP002494DRS005668Ki_meriRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 190; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000>DRS005668DRS005668 �#bunching onionMature pseudostem of 'Aka'aDRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onionDRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11
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�� � �Q ! U =) �)3 W � u�A� �9 3\�[ DRR024741DRR0247412015-12-29��w�DRX022405P�DRX022405DRX022405454 GS FLX Titanium sequencing of PBDRP002820DRS021959454-T_Posterior-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX TitaniumH5DRS021959DRS021959sex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�
Q ! U 3) �)3 W � u�A� �9 3\�[ DRR024743DRR0247432015-12-29��RرDRX022407P�DRX022407DRX022407454 GS FLX Titanium sequencing of HBDRP002820DRS021957454-T_Head-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX TitaniumH3DRS021957DRS021957sex: asexual || strain: GI || sample_title: Dj_GI_HB || tissue_type: Head blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�~ Q ! E ;) �)# G � u�A� �9 3\�[DRR024740DRR0247402015-12-29��<܁�DRX022404P�DRX022404DRX022404454 GS FLX+ sequencing of ABDRP002820DRS021958454-P_Anterior-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX+INSTRUMENT_MODEL: 454 GS FLX+H4DRS021958DRS021958sex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11
h
�� h �Q ! a =)I �Q ) M � u�A� �9 3\�[DRR024737DRR0247372015-12-29 ��� ��LDRX022401P�DRX022401DRX022401Illumina MiSeq paired end sequencing of PBDRP002820DRS021959MiSeq_Posterior-blastemaRNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 316; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 126ILLUMINAIllumina MiSeqINSTRUMENT_MODEL: Illumina MiSeqH5DRS021959DRS021959sex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�vQ ! E 3) �)# G � u�A� �9 3\�[ DRR024744DRR0247442015-12-29�BAiv.DRX022408P�DRX022408DRX022408454 GS FLX+ sequencing of HBDRP002820DRS021957454-P_Head-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX+INSTRUMENT_MODEL: 454 GS FLX+H3DRS021957DRS021957sex: asexual || strain: GI || sample_title: Dj_GI_HB || tissue_type: Head blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�Q ! U ;) �)3 W � u�A� �9 3\�[DRR024739DRR0247392015-12-29" u�DRX022403P�DRX022403DRX022403454 GS FLX Titanium sequencing of ABDRP002820DRS021958454-T_Anterior-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX TitaniumH4DRS021958DRS021958sex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11
{
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DRR024745DRR0247452015-12-29�u $��DRX022404P�DRX022404DRX022404454 GS FLX+ sequencing of ABDRP002820DRS021958454-P_Anterior-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX+INSTRUMENT_MODEL: 454 GS FLX+H4DRS021958DRS021958sex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�Q ! a ;)I �Q ) M � u�A� �9 3] [DRR024736DRR0247362015-12-29 �� [_p&DRX022400P�DRX022400DRX022400Illumina MiSeq paired end sequencing of ABDRP002820DRS021958MiSeq_Anterior-blastemaRNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 338; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 126ILLUMINAIllumina MiSeqINSTRUMENT_MODEL: Illumina MiSeqH4DRS021958DRS021958sex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11
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�� �4P ! )I �Q 3 W �+ ]�W �W O 3k�g�DRR029449DRR0294492015-04-01 ��7 �$yfDRX026509]DRX026509DRX026509Illumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Q�DRS019417DRS019417�sex: mix || strain: Ka4C1 || sample_title: B. xylophilus mixed-stage || description: B.xylophilus mixed-stage on B. cinerea || sample_name: BxMixed || bioproject_id: PRJDB3458 || dev_stage: mixed propagative cDRP002612DRP002612Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected. iDRA002992MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11�yQ ! a 3)I �Q ) M � u�A� �9 3][DRR024738DRR0247382015-12-29 �z7 c��DRX022402P�DRX022402DRX022402Illumina MiSeq paired end sequencing of HBDRP002820DRS021957MiSeq_Head-blastemaRNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 339; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 126ILLUMINAIllumina MiSeqINSTRUMENT_MODEL: Illumina MiSeqH3DRS021957DRS021957sex: asexual || strain: GI || sample_title: Dj_GI_HB || tissue_type: Head blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river�DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.�DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11
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I� �2P ! )I �Q 3 W �+ ]�W �W O 3k�g�DRR029447DRR0294472015-04-01 �+�|�JDRX026507]DRX026507DRX026507Illumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Q�DRS019417DRS019417�sex: mix || strain: Ka4C1 || sample_title: B. xylophilus mixed-stage || description: B.xylophilus mixed-stage on B. cinerea || sample_name: BxMixed || bioproject_id: PRJDB3458 || dev_stage: mixed propagative cDRP002612DRP002612Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected. iDRA002992MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11�4P ! )I �Q 3 W �+ ]�W �W O 3k�g�DRR029448DRR0294482015-04-01 �� ʍ0DRX026508]DRX026508DRX026508Illumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Q�DRS019417DRS019417�sex: mix || strain: Ka4C1 || sample_title: B. xylophilus mixed-stage || description: B.xylophilus mixed-stage on B. cinerea || sample_name: BxMixed || bioproject_id: PRJDB3458 || dev_stage: mixed propagative cDRP002612DRP002612Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected. iDRA002992MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11
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U� �*P ! )I �Q 3 W � ]�W �W O 3k�g�DRR029457DRR0294572017-06-19 �� �/[RDRX026517] DRX026517DRX026517Illumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002610DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Q�DRS019416DRS019416�sex: mix || strain: Ka4C1 || sample_title: B.xylophilus cont Aug || description: B.xylophilus control in August || sample_name: BxContAug || bioproject_id: PRJDB3458 || dev_stage: mixed propagative dDRP002610DRP002610Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected. mDRA002996MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11�(P ! )I �Q 3 W � ]�W �W O 3k�g�DRR029456DRR0294562017-06-19 �R�~�$ DRX026516]
DRX026516DRX026516Illumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002610DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Q�DRS019416DRS019416�sex: mix || strain: Ka4C1 || sample_title: B.xylophilus cont Aug || description: B.xylophilus control in August || sample_name: BxContAug || bioproject_id: PRJDB3458 || dev_stage: mixed propagative dDRP002610DRP002610Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected. mDRA002996MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11
�
S� � P ! i )- �) 3 W � a9�E5�? !U 3w#o�DRR034269DRR0342692015-05-01��..9DRX030902d[DRX030902DRX030902Illumina HiSeq 2000 sequencing of SAMD00029605DRP002638DRS019585LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019585DRS019585�sample_title: LL tomato Time48 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL48 shows 48 hours later with the light. || sample_name: LL48 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�*P ! )I �Q 3 W � ]�W �W O 3k�g�DRR029458DRR0294582017-04-13 ٫� ��b�DRX026518] DRX026518DRX026518Illumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002611DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Q�DRS019416DRS019416�sex: mix || strain: Ka4C1 || sample_title: B.xylophilus cont Aug || description: B.xylophilus control in August || sample_name: BxContAug || bioproject_id: PRJDB3458 || dev_stage: mixed propagative fDRP002611DRP002611Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected. nDRA002997MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11
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`� � P ! i )- �) 3 W � a9�E5�? !U 3w%o�DRR034246DRR0342462015-05-01G
%'_DRX030879dDDRX030879DRX030879Illumina HiSeq 2000 sequencing of SAMD00029589DRP002638DRS019569LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019569DRS019569�sample_title: LL tomato Time2 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL2 shows 2 hours later with the light. || sample_name: LL2 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� P ! i )- �) 3 W � a9�E5�? !U 3w$o�DRR034261DRR0342612015-05-01U�r]�DRX030894dSDRX030894DRX030894Illumina HiSeq 2000 sequencing of SAMD00029596DRP002638DRS019576LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019576DRS019576�sample_title: LL tomato Time32 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL32 shows 32 hours later with the light. || sample_name: LL32 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � P ! i )- �) 3 W � a9�E5�? !U 3w'o�DRR034259DRR0342592015-05-01,I�ҭDRX030892dQDRX030892DRX030892Illumina HiSeq 2000 sequencing of SAMD00029594DRP002638DRS019574LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019574DRS019574�sample_title: LL tomato Time28 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL28 shows 28 hours later with the light. || sample_name: LL28 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� P ! i )- �) 3 W � a9�E5�? !U 3w&o�DRR034262DRR0342622015-05-015��
��>DRX030895dTDRX030895DRX030895Illumina HiSeq 2000 sequencing of SAMD00029597DRP002638DRS019577LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019577DRS019577�sample_title: LL tomato Time34 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL34 shows 34 hours later with the light. || sample_name: LL34 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � !P ! i )- �) 3 W � a9�E5�? !U 3w)o�DRR034266DRR0342662015-05-01LK�3 DRX030899dXDRX030899DRX030899Illumina HiSeq 2000 sequencing of SAMD00029602DRP002638DRS019582LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019582DRS019582�sample_title: LL tomato Time42 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL42 shows 42 hours later with the light. || sample_name: LL42 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� P ! i )- �) 3 W � a9�E5�? !U 3w(o�DRR034256DRR0342562015-05-01E��
�u�DRX030889dNDRX030889DRX030889Illumina HiSeq 2000 sequencing of SAMD00029591DRP002638DRS019571LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019571DRS019571�sample_title: LL tomato Time22 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL22 shows 22 hours later with the light. || sample_name: LL22 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � #P ! i )- �) 3 W � a9�E5�? !U 3w+o�DRR034268DRR0342682015-05-01!�Q�#DRX030901dZDRX030901DRX030901Illumina HiSeq 2000 sequencing of SAMD00029604DRP002638DRS019584LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019584DRS019584�sample_title: LL tomato Time46 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL46 shows 46 hours later with the light. || sample_name: LL46 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� "P ! i )- �) 3 W � a9�E5�? !U 3w*o�DRR034271DRR0342712015-05-01E�
�ӖDRX030904d]DRX030904DRX030904Illumina HiSeq 2000 sequencing of SAMD00029607DRP002638DRS019587LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019587DRS019587�sample_title: LL tomato Time52 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL52 shows 52 hours later with the light. || sample_name: LL52 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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d� � %P ! i )- �) 3 W � a9�E5�? !U 3w-o�DRR034252DRR0342522015-05-012
�cDRX030885dJDRX030885DRX030885Illumina HiSeq 2000 sequencing of SAMD00029586DRP002638DRS019566LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019566DRS019566�sample_title: LL tomato Time14 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL14 shows 14 hours later with the light. || sample_name: LL14 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�$P ! i )- �) 3 W � a9�E5�? !U 3w,o�DRR034249DRR0342492015-05-01%;�j�DRX030882dGDRX030882DRX030882Illumina HiSeq 2000 sequencing of SAMD00029618DRP002638DRS019598LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019598DRS019598�sample_title: LL tomato Time8 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL8 shows 8 hours later with the light. || sample_name: LL8 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � 'P ! i )- �) 3 W � a9�E5�? !U 3w/o�DRR034255DRR0342552015-05-01C3-
c1�DRX030888dMDRX030888DRX030888Illumina HiSeq 2000 sequencing of SAMD00029590DRP002638DRS019570LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019570DRS019570�sample_title: LL tomato Time20 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL20 shows 20 hours later with the light. || sample_name: LL20 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� &P ! i )- �) 3 W � a9�E5�? !U 3w.o�DRR034257DRR0342572015-05-01'�ɲ|DRX030890dODRX030890DRX030890Illumina HiSeq 2000 sequencing of SAMD00029592DRP002638DRS019572LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019572DRS019572�sample_title: LL tomato Time24 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL24 shows 24 hours later with the light. || sample_name: LL24 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � )P ! i )- �) 3 W � a9�E5�? !U 3w1o�DRR034253DRR0342532015-05-01C��
�jDRX030886dKDRX030886DRX030886Illumina HiSeq 2000 sequencing of SAMD00029587DRP002638DRS019567LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019567DRS019567�sample_title: LL tomato Time16 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL16 shows 16 hours later with the light. || sample_name: LL16 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� (P ! i )- �) 3 W � a9�E5�? !U 3w0o�DRR034250DRR0342502015-05-01͡ ��DRX030883dHDRX030883DRX030883Illumina HiSeq 2000 sequencing of SAMD00029584DRP002638DRS019564LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019564DRS019564�sample_title: LL tomato Time10 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL10 shows 10 hours later with the light. || sample_name: LL10 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � +P ! i )- �) 3 W � a9�E5�? !U 3w3o�DRR034254DRR0342542015-05-01W�3q�)DRX030887dLDRX030887DRX030887Illumina HiSeq 2000 sequencing of SAMD00029588DRP002638DRS019568LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019568DRS019568�sample_title: LL tomato Time18 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL18 shows 18 hours later with the light. || sample_name: LL18 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� *P ! i )- �) 3 W � a9�E5�? !U 3w2o�DRR034267DRR0342672015-05-01A��
�tDRX030900dYDRX030900DRX030900Illumina HiSeq 2000 sequencing of SAMD00029603DRP002638DRS019583LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019583DRS019583�sample_title: LL tomato Time44 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL44 shows 44 hours later with the light. || sample_name: LL44 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � -P ! i )- �) 3 W � a9�E5�? !U 3w5o�DRR034258DRR0342582015-05-016?,
Ε�DRX030891dPDRX030891DRX030891Illumina HiSeq 2000 sequencing of SAMD00029593DRP002638DRS019573LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019573DRS019573�sample_title: LL tomato Time26 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL26 shows 26 hours later with the light. || sample_name: LL26 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� ,P ! i )- �) 3 W � a9�E5�? !U 3w4o�DRR034260DRR0342602015-05-01%i�t�DRX030893dRDRX030893DRX030893Illumina HiSeq 2000 sequencing of SAMD00029595DRP002638DRS019575LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019575DRS019575�sample_title: LL tomato Time30 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL30 shows 30 hours later with the light. || sample_name: LL30 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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d� � /P ! i )- �) 3 W � a9�E5�? !U 3w7o�DRR034264DRR0342642015-05-01Pl��oDRX030897dVDRX030897DRX030897Illumina HiSeq 2000 sequencing of SAMD00029599DRP002638DRS019579LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019579DRS019579�sample_title: LL tomato Time38 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL38 shows 38 hours later with the light. || sample_name: LL38 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�.P ! i )- �) 3 W � a9�E5�? !U 3w6o�DRR034247DRR0342472015-05-01!���DRX030880dEDRX030880DRX030880Illumina HiSeq 2000 sequencing of SAMD00029600DRP002638DRS019580LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019580DRS019580�sample_title: LL tomato Time4 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL4 shows 4 hours later with the light. || sample_name: LL4 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � 1P ! i )- �) 3 W � a9�E5�? !U 3w9o�DRR034272DRR0342722015-05-01J|a��SDRX030905d^DRX030905DRX030905Illumina HiSeq 2000 sequencing of SAMD00029608DRP002638DRS019588LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019588DRS019588�sample_title: LL tomato Time54 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL54 shows 54 hours later with the light. || sample_name: LL54 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� 0P ! i )- �) 3 W � a9�E5�? !U 3w8o�DRR034277DRR0342772015-05-01# ��'lDRX030910dcDRX030910DRX030910Illumina HiSeq 2000 sequencing of SAMD00029614DRP002638DRS019594LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019594DRS019594�sample_title: LL tomato Time64 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL64 shows 64 hours later with the light. || sample_name: LL64 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � 3P ! i )- �) 3 W � a9�E5�? !U 3w;o�DRR034279DRR0342792015-05-014
`3�DRX030912deDRX030912DRX030912Illumina HiSeq 2000 sequencing of SAMD00029616DRP002638DRS019596LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019596DRS019596�sample_title: LL tomato Time68 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL68 shows 68 hours later with the light. || sample_name: LL68 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� 2P ! i )- �) 3 W � a9�E5�? !U 3w:o�DRR034280DRR0342802015-05-01&�����DRX030913dfDRX030913DRX030913Illumina HiSeq 2000 sequencing of SAMD00029617DRP002638DRS019597LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019597DRS019597�sample_title: LL tomato Time70 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL70 shows 70 hours later with the light. || sample_name: LL70 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � 5P ! i )- �) 3 W � a9�E5�? !U 3w=o�DRR034263DRR0342632015-05-01\(�\vDRX030896dUDRX030896DRX030896Illumina HiSeq 2000 sequencing of SAMD00029598DRP002638DRS019578LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019578DRS019578�sample_title: LL tomato Time36 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL36 shows 36 hours later with the light. || sample_name: LL36 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� 4P ! i )- �) 3 W � a9�E5�? !U 3w<o�DRR034251DRR0342512015-05-012� � DRX030884dIDRX030884DRX030884Illumina HiSeq 2000 sequencing of SAMD00029585DRP002638DRS019565LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019565DRS019565�sample_title: LL tomato Time12 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL12 shows 12 hours later with the light. || sample_name: LL12 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � 7P ! i )- �) 3 W � a9�E5�? !U 3w?o�DRR034276DRR0342762015-05-01R�.u�*DRX030909dbDRX030909DRX030909Illumina HiSeq 2000 sequencing of SAMD00029613DRP002638DRS019593LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019593DRS019593�sample_title: LL tomato Time62 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL62 shows 62 hours later with the light. || sample_name: LL62 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� 6P ! i )- �) 3 W � a9�E5�? !U 3w>o�DRR034275DRR0342752015-05-01�j�� DRX030908daDRX030908DRX030908Illumina HiSeq 2000 sequencing of SAMD00029612DRP002638DRS019592LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019592DRS019592�sample_title: LL tomato Time60 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL60 shows 60 hours later with the light. || sample_name: LL60 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � 9P ! i )- �) 3 W � a9�E5�? !U 3wAo�DRR034270DRR0342702015-05-018�~ J]DRX030903d\DRX030903DRX030903Illumina HiSeq 2000 sequencing of SAMD00029606DRP002638DRS019586LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019586DRS019586�sample_title: LL tomato Time50 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL50 shows 50 hours later with the light. || sample_name: LL50 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� 8P ! i )- �) 3 W � a9�E5�? !U 3w@o�DRR034278DRR0342782015-05-01"��uqDRX030911ddDRX030911DRX030911Illumina HiSeq 2000 sequencing of SAMD00029615DRP002638DRS019595LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019595DRS019595�sample_title: LL tomato Time66 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL64 shows 64 hours later with the light. || sample_name: LL66 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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d� �;P ! i )- �) 3 W � a9�E5�? !U 3wCo�DRR034245DRR0342452015-05-01 ��9![DRX030878dCDRX030878DRX030878Illumina HiSeq 2000 sequencing of SAMD00029583DRP002638DRS019563LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019563DRS019563�sample_title: LL tomato Time0 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL0 shows the moment with the light. || sample_name: LL0 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�:P ! i )- �) 3 W � a9�E5�? !U 3wBo�DRR034248DRR0342482015-05-01.�� [#�DRX030881dFDRX030881DRX030881Illumina HiSeq 2000 sequencing of SAMD00029611DRP002638DRS019591LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019591DRS019591�sample_title: LL tomato Time6 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL6 shows 6 hours later with the light. || sample_name: LL6 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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`� � =P ! i )- �) 3 W � a9�E5�? !U 3wEo�DRR034274DRR0342742015-05-01=�� H�DRX030907d`DRX030907DRX030907Illumina HiSeq 2000 sequencing of SAMD00029610DRP002638DRS019590LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019590DRS019590�sample_title: LL tomato Time58 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL58 shows 58 hours later with the light. || sample_name: LL58 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11� <P ! i )- �) 3 W � a9�E5�? !U 3wDo�DRR034273DRR0342732015-05-01,wd���DRX030906d_DRX030906DRX030906Illumina HiSeq 2000 sequencing of SAMD00029609DRP002638DRS019589LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019589DRS019589�sample_title: LL tomato Time56 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL56 shows 56 hours later with the light. || sample_name: LL56 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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` � >P ! i )- �) 3 W � a9�E5�? !U 3wFo�DRR034265DRR0342652015-05-01��L/DRX030898dWDRX030898DRX030898Illumina HiSeq 2000 sequencing of SAMD00029601DRP002638DRS019581LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000W�DRS019581DRS019581�sample_title: LL tomato Time40 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL40 shows 40 hours later with the light. || sample_name: LL40 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu
DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.
�DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
4 4 �I?S M !oE E G!}G/ �- �) C g �S} �C �9! G G�m�O + 3g� �JE-MTAB-387:Early_Exponential.txtERR0196522016-06-28bKu
ҜtGenomics Core Facility, EMBL, Heidelberg, GermanyE-MTAB-387:Early_Exponential �JE-MTAB-387:Early_ExponentialERX007970RNA sequencing in E. coli K12E-MTAB-387E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Early_exponentialRNA sequencing in E. coli K12Early_ExponentialOTHEROTHERcDNASINGLE - The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: GENOTYPE: wide_type || Experimental Factor: GROWTHCONDITION: early-exponential �]E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Early_exponentialERS0161162Protocols: The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).Organism: Escherichia coli || StrainOrLine: K-12 substr. MG1655 || Genotype: wide_type �E-MTAB-387ERP000350RNA sequencing in E. coli K12OtherRNA sequencing in E. coli K12Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phaseE-MTAB-387 in ArrayExpress: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MTAB-3872�ERA014184EMBL_HeidelbergEBI2018-05-10 18:11:11
� � �@U [ !oS S G!� G= �- �) C g �m� �C �9! G G�m�O + 3g� �KE-MTAB-387:Transition_to_Stationary.txtERR0196532016-06-28l��La�Genomics Core Facility, EMBL, Heidelberg, GermanyE-MTAB-387:Transition_to_Stationary �IE-MTAB-387:Transition_to_StationaryERX007969RNA sequencing in E. coli K12E-MTAB-387E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationaryRNA sequencing in E. coli K12Transition_to_StationaryOTHEROTHERcDNASINGLE - The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: GENOTYPE: wide_type || Experimental Factor: GROWTHCONDITION: transition-to-stationary-phase �\E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationaryERS0161152Protocols: The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).Organism: Escherichia coli || StrainOrLine: K-12 substr. MG1655 || Genotype: wide_type �E-MTAB-387ERP000350RNA sequencing in E. coli K12OtherRNA sequencing in E. coli K12Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phaseE-MTAB-387 in ArrayExpress: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MTAB-3872�ERA014184EMBL_HeidelbergEBI2018-05-10 18:11:11 esis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber cortex �E-MTAB-552:Tuber cortexERS023602Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber cortex || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11
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�kEV ; !C- - �S!7�) � �) C g g7 �' �9! �9 ���5 1 3���E-MTAB-552:RHs13.txt.gzERR0299212016-08-09 �����Aalborg University, DenmarkE-MTAB-552:RHs13 �?E-MTAB-552:RHs13ERX010649Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Tuber peelTranscriptome Analysis of the potato (genotype RH89-039-16)S13WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time ڦ,DW ; !C- - �M!;�) � �) = a �C; �' �k! �9 ���5 1 3���E-MTAB-552:RHs08.txt.gzERR0299162016-08-09`7
�+�Aalborg University, DenmarkE-MTAB-552:RHs08 �3E-MTAB-552:RHs08ERX010637Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Mature TuberTranscriptome Analysis of the potato (genotype RH89-039-16)S8WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower bud ٥[CV ; !C- - �S!/�) � �) C g _/ �' �1! �9 ���5 1 3���E-MTAB-552:RHs10.txt.gzERR0299182016-08-09 �b���$Aalborg University, DenmarkE-MTAB-552:RHs10 �8E-MTAB-552:RHs10ERX010642Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:StamenTranscriptome Analysis of the potato (genotype RH89-039-16)S10WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around t إPBV ; !C- - �M!/�) � �) = a _/ �' �1! �9 ���5 1 3���E-MTAB-552:RHs01.txt.gzERR0299092016-08-09]��
)z(Aalborg University, DenmarkE-MTAB-552:RHs01 �9E-MTAB-552:RHs01ERX010643Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:FlowerTranscriptome Analysis of the potato (genotype RH89-039-16)S1WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Ar ץsAV ; !C- - �S!;�) � �) C g k; �' �=! �9 ���5 1 3���E-MTAB-552:RHs16.txt.gzERR0299242016-08-09 �7�7� Aalborg University, DenmarkE-MTAB-552:RHs16 �<E-MTAB-552:RHs16ERX010646Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Tuber cortexTranscriptome Analysis of the potato (genotype RH89-039-16)S16WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anth � ound the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: flower �E-MTAB-552:FlowerERS023599Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: flower || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 he same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: stamen �E-MTAB-552:StamenERS023598Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stamen || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 s were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: tuber || Experimental Factor: DEVELOPMENTALSTAGE: mature ��E-MTAB-552:Mature TuberERS023593Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber || DevelopmentalStage: mature || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 , anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber peel �E-MTAB-552:Tuber peelERS023605Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber peel || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 r). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: stem � E-MTAB-552:StemERS023607Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stem || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11
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-
PZ\} �TJV ; !C- - �M!1�) � �) = a a1 �' �3! �9 ���5 1 3���E-MTAB-552:RHs03.txt.gzERR0299112016-08-09c�
W<Aalborg University, DenmarkE-MTAB-552:RHs03 �;E-MTAB-552:RHs03ERX010645Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:PetioleTranscriptome Analysis of the potato (genotype RH89-039-16)S3WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Aroun �sIV ; !C- - �S!;�) � �) C g k; �' �=! �9 ���5 1 3���E-MTAB-552:RHs15.txt.gzERR0299232016-08-09 ���r�Aalborg University, DenmarkE-MTAB-552:RHs15 �4E-MTAB-552:RHs15ERX010638Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Tuber sproutTranscriptome Analysis of the potato (genotype RH89-039-16)S15WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anth ߥkHV ; !C- - �S!7�) � �) C g g7 �' �9! �9 ���5 1 3���E-MTAB-552:RHs12.txt.gzERR0299202016-08-09 ��x&��Aalborg University, DenmarkE-MTAB-552:RHs12 �6E-MTAB-552:RHs12ERX010640Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Tuber pithTranscriptome Analysis of the potato (genotype RH89-039-16)S12WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time ޥRGV ; !C- - �S!+�) � �) C g [+ �' �-! �9 ���5 1 3���E-MTAB-552:RHs09.txt.gzERR0299172016-08-09 �L2��Aalborg University, DenmarkE-MTAB-552:RHs09 �=E-MTAB-552:RHs09ERX010647Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:RootTranscriptome Analysis of the potato (genotype RH89-039-16)S9WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Ar ݥHFV ; !C- - �M!+�) � �) = a [+ �' �-! �9 ���5 1 3���E-MTAB-552:RHs05.txt.gzERR0299132016-08-09_�<
w�pAalborg University, DenmarkE-MTAB-552:RHs05 �AE-MTAB-552:RHs05ERX010651Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:StemTranscriptome Analysis of the potato (genotype RH89-039-16)S5WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tube � ound the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: root �E-MTAB-552:RootERS023603Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: root || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 , anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber pith �E-MTAB-552:Tuber pithERS023596Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber pith || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 esis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber sprout ��E-MTAB-552:Tuber sproutERS023594Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber sprout || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 d the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: petiole �E-MTAB-552:PetioleERS023601Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: petiole || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: tuber || Experimental Factor: DEVELOPMENTALSTAGE: young ��E-MTAB-552:Young TuberERS023595Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber || DevelopmentalStage: young || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11
� � �4 � �*OW ; !C- - �S!I�) � �) C g �KI �' �-! �9 ���5 1 3���E-MTAB-552:RHs11.txt.gzERR0299192016-08-09 �f`Ze�Aalborg University, DenmarkE-MTAB-552:RHs11 �>E-MTAB-552:RHs11ERX010648Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Water stressed leafTranscriptome Analysis of the potato (genotype RH89-039-16)S11WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and develop �PNV ; !C- - �M!/�) � �) = a _/ �' �1! �9 ���5 1 3���E-MTAB-552:RHs06.txt.gzERR0299142016-08-09e<4<wPAalborg University, DenmarkE-MTAB-552:RHs06 �:E-MTAB-552:RHs06ERX010644Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:StolonTranscriptome Analysis of the potato (genotype RH89-039-16)S6WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Ar �HMV ; !C- - �M!+�) � �) = a [+ �' �-! �9 ���5 1 3���E-MTAB-552:RHs02.txt.gzERR0299102016-08-09f'�]��Aalborg University, DenmarkE-MTAB-552:RHs02 �7E-MTAB-552:RHs02ERX010641Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:LeafTranscriptome Analysis of the potato (genotype RH89-039-16)S2WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tube �`LV ; !C- - �M!7�) � �) = a g7 �' �9! �9 ���5 1 3���E-MTAB-552:RHs04.txt.gzERR0299122016-08-09\�Z
(�Aalborg University, DenmarkE-MTAB-552:RHs04 �@E-MTAB-552:RHs04ERX010650Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Shoot apexTranscriptome Analysis of the potato (genotype RH89-039-16)S4WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the sam �(KW ; !C- - �M!9�) � �) = a �A9 �' �i! �9 ���5 1 3���E-MTAB-552:RHs07.txt.gzERR0299152016-08-09`Ұ
���Aalborg University, DenmarkE-MTAB-552:RHs07 �5E-MTAB-552:RHs07ERX010639Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Young TuberTranscriptome Analysis of the potato (genotype RH89-039-16)S7WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower � e time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: shoot apex �E-MTAB-552:Shoot apexERS023606Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: shoot apex || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 r). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: leaf �E-MTAB-552:LeafERS023597Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: leaf || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 ound the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: stolon �E-MTAB-552:StolonERS023600Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stolon || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 ing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: leaf || Experimental Factor: GROWTHCONDITION: water stressed �E-MTAB-552:Water stressed leafERS023604Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: leaf || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11 r buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: whole plant || Experimental Factor: GROWTHCONDITION: in vitro �E-MTAB-552:Whole in vitro plantERS023608Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: whole plant || BioSourceType: fresh_sample
~E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552M�ERA021569AAUAalborg University2018-05-10 18:11:11
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�2QR A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3ѾTuE-MTAB-861:21days.fastq.gzERR0564802016-06-283�
��GATC BIOTECH AGE-MTAB-861:assay 4 ��E-MTAB-861:assay 4ERX033523wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 4wheat starchy endosperm RNA-SeqRNA Extract 4RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 21 d WE-MTAB-861:Central starchy endosperm 4ERS074999�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 21 d || OrganismPart: starchy endosperm�E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861 ��ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11�3PW ; !C- - �S!K�) � �) C g �MK �' �;! �9 ���5 1 3���E-MTAB-552:RHs14.txt.gzERR0299222016-08-09~�� @Aalborg University, DenmarkE-MTAB-552:RHs14 �BE-MTAB-552:RHs14ERX010652Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Whole in vitro plantTranscriptome Analysis of the potato (genotype RH89-039-16)S14WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flowe �
K K �2RR A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3ѿTtE-MTAB-861:17days.fastq.gzERR0564792016-06-28-� jKGATC BIOTECH AGE-MTAB-861:assay 3 �E-MTAB-861:assay 3ERX033527wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 3wheat starchy endosperm RNA-SeqRNA Extract 3RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 17 d [E-MTAB-861:Central starchy endosperm 3ERS075003�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 17 d || OrganismPart: starchy endosperm�E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861 ��ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11
K K �2SR A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3�TvE-MTAB-861:28days.fastq.gzERR0564812016-06-289��wGATC BIOTECH AGE-MTAB-861:assay 5 �E-MTAB-861:assay 5ERX033525wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 5wheat starchy endosperm RNA-SeqRNA Extract 5RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 28 d YE-MTAB-861:Central starchy endosperm 5ERS075001�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 28 d || OrganismPart: starchy endosperm�E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861 ��ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11
K K �2TR A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3�TrE-MTAB-861:10days.fastq.gzERR0564772016-06-28Q� �GATC BIOTECH AGE-MTAB-861:assay 1 �E-MTAB-861:assay 1ERX033526wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 1wheat starchy endosperm RNA-SeqRNA Extract 1RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 10 d ZE-MTAB-861:Central starchy endosperm 1ERS075002�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 10 d || OrganismPart: starchy endosperm�E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861 ��ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11
K K �2UR A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3��TsE-MTAB-861:14days.fastq.gzERR0564782016-06-282<
�0GATC BIOTECH AGE-MTAB-861:assay 2 �E-MTAB-861:assay 2ERX033524wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 2wheat starchy endosperm RNA-SeqRNA Extract 2RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 14 d XE-MTAB-861:Central starchy endosperm 2ERS075000�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 14 d || OrganismPart: starchy endosperm�E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861 ��ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11
a a � VV = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3�$� E-MTAB-1585:7sk_1b.fq.gzERR2474162016-06-28 �Dq1B��ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_1bF�E-MTAB-1585:7sk_1bERX221956Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_1bTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_1bRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneC�E-MTAB-1585:7sk_1bERS225457'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 ) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)C�E-MTAB-1585:7sk_6cERS225454'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
�KXW = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3�&�E-MTAB-1585:7sk_6a.fq.gzERR2474212016-06-28 �8�!�YhROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_6aF�E-MTAB-1585:7sk_6aERX221947Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_6aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_6aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) �MWW = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3�%�E-MTAB-1585:7sk_6c.fq.gzERR2474122016-06-28 �� �*0�ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_6cF�E-MTAB-1585:7sk_6cERX221953Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_6cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_6cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002 � were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)C�E-MTAB-1585:7sk_6aERS225448'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
a a � YV = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3�'�E-MTAB-1585:7sk_1a.fq.gzERR2474112016-06-28
|(5��ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_1aF�E-MTAB-1585:7sk_1aERX221952Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_1aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_1aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneC�E-MTAB-1585:7sk_1aERS225453'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)C�E-MTAB-1585:7sk_2cERS225452'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
�K[W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3�)�E-MTAB-1585:7sk_2b.fq.gzERR2474192016-06-28 �.�\ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_2bF�E-MTAB-1585:7sk_2bERX221957Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_2bTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_2bRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) �KZW = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3�(�
E-MTAB-1585:7sk_2c.fq.gzERR2474172016-06-281
oř1ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_2cF�E-MTAB-1585:7sk_2cERX221951Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_2cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_2cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) � were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)C�E-MTAB-1585:7sk_2bERS225458'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
b b �\V = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3�*�E-MTAB-1585:7sk_4a.fq.gzERR2474102016-06-28H;�c�ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_4aF�E-MTAB-1585:7sk_4aERX221948Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_4aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_4aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneC�E-MTAB-1585:7sk_4aERS225449'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
_ _ � ]V = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3�+� E-MTAB-1585:7sk_1c.fq.gzERR2474132016-06-28�y� �^6�ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_1cF�E-MTAB-1585:7sk_1cERX221945Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_1cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_1cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneC�E-MTAB-1585:7sk_1cERS225446'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)C�E-MTAB-1585:7sk_2aERS225456'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
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E-MTAB-1585:7sk_5a.fq.gzERR2474142016-06-28N����>ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_5aF�E-MTAB-1585:7sk_5aERX221946Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_5aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_5aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) w ��J`W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3�.�E-MTAB-1585:7sk_3a.fq.gzERR2474202016-06-28k<�]$�ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_3aF�E-MTAB-1585:7sk_3aERX221944Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_3aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_3aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) w ��K_W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3�-�E-MTAB-1585:7sk_3c.fq.gzERR2474182016-06-28+$u;�COROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_3cF�E-MTAB-1585:7sk_3cERX221954Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_3cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_3cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) ��K^W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3�,�E-MTAB-1585:7sk_2a.fq.gzERR2474232016-06-28 �'(x�eROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_2aF�E-MTAB-1585:7sk_2aERX221955Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_2aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_2aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) � were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)C�E-MTAB-1585:7sk_3cERS225455'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 ere cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)C�E-MTAB-1585:7sk_3aERS225445'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 ere cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)C�E-MTAB-1585:7sk_5aERS225447'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
a a � bV = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3�0� E-MTAB-1585:7sk_4c.fq.gzERR2474152016-06-28DzH@�\XROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_4cF�E-MTAB-1585:7sk_4cERX221949Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_4cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_4cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneC�E-MTAB-1585:7sk_4cERS225450'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)C�E-MTAB-1585:7sk_5cERS225451'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal�E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585u�ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
�
�~� �\fM = !! = = A / ) ' �) # G / % /%]] 5 3"��grun_AIG_AOSS_7_42RALAAXXERR2603762009-09-212016-06-28 ��O��Genoscopeexp_AIG_AOSS_7_42RALAAXXj�exp_AIG_AOSS_7_42RALAAXXERX234948Adineta vaga GA IIx Simplestudy_AIGsample_AIG_104782AIGAOSSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none providedREAD_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAunspecifiedINSTRUMENT_MODEL: unspecifiedb"sample_AIG_104782ERS235800�NAdineta vagastudy_AIGERP002474Adineta_vaga_cdnaMetagenomicsTranscriptome sequencing of Adineta vagaAIGTranscriptome sequencing of Adineta vagaLinked publication: http://dx.doi.org/10.1038/nature12326{�ERA206999GSCThe Genoscope center2018-05-10 18:11:11�FeM E !! E E E / ) ' �I3 W / % /%]] 5 3"��hrun_1.GAC.AIG_AOTS_GWDJGJ101ERR2603772011-01-202016-06-28�
4G�Genoscopeexp_1.GAC.AIG_AOTS_GWDJGJ101j�exp_1.GAC.AIG_AOTS_GWDJGJ101ERX234949Adineta vaga Titanium Simplestudy_AIGsample_AIG_104782AIGAOTSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none providedREAD_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX Titaniumb"sample_AIG_104782ERS235800�NAdineta vagastudy_AIGERP002474Adineta_vaga_cdnaMetagenomicsTranscriptome sequencing of Adineta vagaAIGTranscriptome sequencing of Adineta vagaLinked publication: http://dx.doi.org/10.1038/nature12326{�ERA206999GSCThe Genoscope center2018-05-10 18:11:11�FdM E !! E E E / ) ' �I3 W / % /%]] 5 3"��irun_2.GAC.AIG_AOTS_GWDJGJ102ERR2603782011-01-202016-06-28��
�Genoscopeexp_2.GAC.AIG_AOTS_GWDJGJ102j�exp_2.GAC.AIG_AOTS_GWDJGJ102ERX234950Adineta vaga Titanium Simplestudy_AIGsample_AIG_104782AIGAOTSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none providedREAD_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX Titaniumb"sample_AIG_104782ERS235800�NAdineta vagastudy_AIGERP002474Adineta_vaga_cdnaMetagenomicsTranscriptome sequencing of Adineta vagaAIGTranscriptome sequencing of Adineta vagaLinked publication: http://dx.doi.org/10.1038/nature12326{�ERA206999GSCThe Genoscope center2018-05-10 18:11:11�KcW = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3�1�E-MTAB-1585:7sk_5c.fq.gzERR2474222016-06-28g��G��JROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_5cF�E-MTAB-1585:7sk_5cERX221950Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_5cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_5cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) �
� �� �&hP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]yw�EUPZL4S01SRR0006562007-08-282013-07-25���7 WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�Z2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�$gP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]xw�EUEMSW407SRR0006502007-08-222013-07-25�(]WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�[2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
� �� �$jP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]{w�EUEMSW402SRR0006542007-08-222013-07-25ʃWUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�Z2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�$iP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]zw�EUEMSW403SRR0006532007-08-222013-07-25 b ��WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�Z2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
� �� �$lP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]}w�EUEMSW401SRR0006522007-08-222013-07-25 W0WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�Z2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�$kP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]|w�EUEMSW404SRR0006512007-08-222013-07-25�_oWUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�Z2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
� �� �&nP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]w�EUGXWLM02SRR0006492007-08-232013-07-25 ;/�WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�[2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�&mP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]~w�EUPZL4S02SRR0006582007-08-282013-07-25���ώWUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�[2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
� �� �$pP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]�w�EUEMSW405SRR0006482007-08-222013-07-25z��WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�[2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�$oP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]�w�EUEMSW406SRR0006572007-08-222013-07-25Vt�WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�[2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
� �� �&rP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]�w�EUGXWLM01SRR0006472007-08-232013-07-25��=�WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�Z2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�$qP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3]�w�EUEMSW408SRR0006552007-08-222013-07-25 n ��WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�[2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241 �yTachyglossus aculeatusSRS000290$-none provided>{2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910��SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
� � �MsU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3]�w�EXRHO8E06SRR0001422007-10-232013-01-31 � �WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�a2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246 �~20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba>�2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331��SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �MtU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3]�w�EXRHO8E07SRR0001392007-10-232013-01-31��AWUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�a2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246 �~20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba>�2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331��SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �OuU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3]�w�EZNCMKS01SRR0001412007-11-282013-01-31/�s8�WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�a2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246 �~20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba>�2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331��SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �MvU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3]�w�EXRHO8E08SRR0001382007-10-232013-01-31W&�WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�a2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246 �~20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba>�2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331��SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �OwU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3]�w�EZNCMKS02SRR0001402007-11-282013-01-31�7���WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�a2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246 �~20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba>�2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331��SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �MxU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3]�w�EXRHO8E05SRR0001372007-10-232013-01-31 < ��WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAG�a2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246 �~20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba>�2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331��SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� F� �7zS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�q��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.3SRR0182582014-06-09 魼]8�BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26770.0 || instrument_name: SL-XAN || lane: 3 || lsid: BROAD:SEQUENCING_SAMPLE:26770.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302�30BV1AAXX080828-3-PSRX006124Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7010' containing sample 'M990514'Illumina sequencing of Homo sapiens via complementary DNASolexa-7010RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26770.0 || lsid: BROAD:SEQUENCING_SAMPLE:26770.0 || material_type: New Tech Library || project: G1681 || work_request: 17302 ��PRJNA39289.M990514SRS003455%�n/an/an/aSample name: M990514 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�7yS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�p��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.7SRR0182612014-06-09 ��_� �BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26767.0 || instrument_name: SL-XAN || lane: 7 || lsid: BROAD:SEQUENCING_SAMPLE:26767.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302�30BV1AAXX080828-7-PSRX006127Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7007' containing sample 'M980409'Illumina sequencing of Homo sapiens via complementary DNASolexa-7007RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26767.0 || lsid: BROAD:SEQUENCING_SAMPLE:26767.0 || material_type: New Tech Library || project: G1681 || work_request: 17302 ��PRJNA39289.M980409SRS003458%�n/an/an/aSample name: M980409 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
� D� �8|S � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�s��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.3SRR0182652014-06-09|�.1��TBIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26765.0 || instrument_name: SL-XAN || lane: 3 || lsid: BROAD:SEQUENCING_SAMPLE:26765.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461�30C3WAAXX080918-3-PSRX006131Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7005' containing sample 'M010403'Illumina sequencing of Homo sapiens via complementary DNASolexa-7005RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26765.0 || lsid: BROAD:SEQUENCING_SAMPLE:26765.0 || material_type: New Tech Library || project: G1681 || work_request: 17461 ��PRJNA39289.M010403SRS003460%�n/an/an/aSample name: M010403 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�9{S � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�r��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.6SRR0182672014-06-09 �ƣW�$�BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26774.0 || instrument_name: SL-XAN || lane: 6 || lsid: BROAD:SEQUENCING_SAMPLE:26774.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461�30C3WAAXX080918-6-PSRX006133Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7014' containing sample 'M000921'Illumina sequencing of Homo sapiens via complementary DNASolexa-7014RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26774.0 || lsid: BROAD:SEQUENCING_SAMPLE:26774.0 || material_type: New Tech Library || project: G1681 || work_request: 17461 ��PRJNA39289.M000921SRS003462%�n/an/an/aSample name: M000921 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
� F� �7~S � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�u��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.8SRR0182622014-06-09 �@_��BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26766.0 || instrument_name: SL-XAN || lane: 8 || lsid: BROAD:SEQUENCING_SAMPLE:26766.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302�30BV1AAXX080828-8-PSRX006128Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7006' containing sample 'M970109'Illumina sequencing of Homo sapiens via complementary DNASolexa-7006RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26766.0 || lsid: BROAD:SEQUENCING_SAMPLE:26766.0 || material_type: New Tech Library || project: G1681 || work_request: 17302 ��PRJNA39289.M970109SRS003459%�n/an/an/aSample name: M970109 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�7}S � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�t��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.6SRR0182602014-06-09 �)�a���BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26768.0 || instrument_name: SL-XAN || lane: 6 || lsid: BROAD:SEQUENCING_SAMPLE:26768.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302�30BV1AAXX080828-6-PSRX006126Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7008' containing sample 'M990802'Illumina sequencing of Homo sapiens via complementary DNASolexa-7008RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26768.0 || lsid: BROAD:SEQUENCING_SAMPLE:26768.0 || material_type: New Tech Library || project: G1681 || work_request: 17302 ��PRJNA39289.M990802SRS003457%�n/an/an/aSample name: M990802 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
� G� �0� S � ! �!3 �a #)I �# C g �E+ � 9 C�y% I / 3�w��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.1SRR0182632014-06-09 �b]V�1BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 1 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17462�30C3WAAXX080918-1-PSRX006129Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'Illumina sequencing of Homo sapiens via complementary DNASolexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17462 ��PRJNA39289.MEWOSRS003453%�n/an/an/aSample name: MEWO || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�6S � ! �!3 �g #)I �# C g �E1 � 9 C�y% I / 3�v��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.7SRR0182682014-06-09 �^H(�BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26775.0 || instrument_name: SL-XAN || lane: 7 || lsid: BROAD:SEQUENCING_SAMPLE:26775.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461�30C3WAAXX080918-7-PSRX006134Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7015' containing sample 'K-562-4'Illumina sequencing of Homo sapiens via complementary DNASolexa-7015RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26775.0 || lsid: BROAD:SEQUENCING_SAMPLE:26775.0 || material_type: New Tech Library || project: G1681 || work_request: 17461 ��PRJNA39289.K-562-4SRS003463%�n/an/an/aSample name: K-562-4 || geographic location (country and/or sea,region): missing || isolation source: K-562 || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
� E� �9�S � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�y��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.5SRR0182662014-06-09 �VZStDBIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26773.0 || instrument_name: SL-XAN || lane: 5 || lsid: BROAD:SEQUENCING_SAMPLE:26773.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461�30C3WAAXX080918-5-PSRX006132Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7013' containing sample '501 MEL'Illumina sequencing of Homo sapiens via complementary DNASolexa-7013RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26773.0 || lsid: BROAD:SEQUENCING_SAMPLE:26773.0 || material_type: New Tech Library || project: G1681 || work_request: 17461 ��PRJNA39289.501 MELSRS003461%�n/an/an/aSample name: 501 MEL || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�7�S � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�x��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.5SRR0182592014-06-09 Ӝ�TP\�BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26769.0 || instrument_name: SL-XAN || lane: 5 || lsid: BROAD:SEQUENCING_SAMPLE:26769.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302�30BV1AAXX080828-5-PSRX006125Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7009' containing sample 'M000216'Illumina sequencing of Homo sapiens via complementary DNASolexa-7009RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26769.0 || lsid: BROAD:SEQUENCING_SAMPLE:26769.0 || material_type: New Tech Library || project: G1681 || work_request: 17302 ��PRJNA39289.M000216SRS003456%�n/an/an/aSample name: M000216 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
� N� �6�S � ! �!3 �g #)I �# C g �E1 � 9 C�y% I / 3�{��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.8SRR0182692014-06-09 �É`S�BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26776.0 || instrument_name: SL-XAN || lane: 8 || lsid: BROAD:SEQUENCING_SAMPLE:26776.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461�30C3WAAXX080918-8-PSRX006135Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7016' containing sample 'K-562-3'Illumina sequencing of Homo sapiens via complementary DNASolexa-7016RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 350; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26776.0 || lsid: BROAD:SEQUENCING_SAMPLE:26776.0 || material_type: New Tech Library || project: G1681 || work_request: 17461 ��PRJNA39289.K-562-3SRS003464%�n/an/an/aSample name: K-562-3 || geographic location (country and/or sea,region): missing || isolation source: K-562 || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�.�S � ! �!3 �a #)I �# C g �E+ � 9 C�y% I / 3�z�BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.1SRR0182562014-06-09 ��O�N$BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 1 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302�30BV1AAXX080828-1-PSRX006122Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'Illumina sequencing of Homo sapiens via complementary DNASolexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17302 ��PRJNA39289.MEWOSRS003453%�n/an/an/aSample name: MEWO || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
� E� �0�S � ! �!3 �a #)I �# C g �E+ � 9 C�y% I / 3�}��BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.2SRR0182642014-06-09 ��YB��BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 2 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17462�30C3WAAXX080918-2-PSRX006130Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'Illumina sequencing of Homo sapiens via complementary DNASolexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17462 ��PRJNA39289.MEWOSRS003453%�n/an/an/aSample name: MEWO || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�7�S � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3�|��BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.2SRR0182572014-06-09 �cZ��rBIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26771.0 || instrument_name: SL-XAN || lane: 2 || lsid: BROAD:SEQUENCING_SAMPLE:26771.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302�30BV1AAXX080828-2-PSRX006123Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7011' containing sample 'M980928'Illumina sequencing of Homo sapiens via complementary DNASolexa-7011RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26771.0 || lsid: BROAD:SEQUENCING_SAMPLE:26771.0 || material_type: New Tech Library || project: G1681 || work_request: 17302 ��PRJNA39289.M980928SRS003454%�n/an/an/aSample name: M980928 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missingC�Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501��SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11 Adapter A_For primer (5’CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGT3’), 25 µM Adapter B_For primer (5’CCTATCCCCTGTGTGCCTTGGCAGTCTCAGT3’), 3% DMSO, 10 mM dNTPs and 1 U Phusion polymerase (Finnzymes/NEB, USA). The PCR conditions were as follows: 980C for 30 seconds, followed by 15 cycles with 980C for 10 seconds, 680C for 30 seconds and 720C for 30 seconds, with a final extension of 720C for 5 minute and cleaned up with a Qiaquick minelute PCR column. Normalization of cDNA library The cDNA library was normalized according to the protocol described in the Trimmer Direct Kit (Evrogen, Russia). In brief, 300 ng of cDNA were incubated at 950C for 5 minutes followed by incubation at 680C for 4 hours in the hybridization buffer included in the kit (50 mM Hepes, pH7.5 and 0.5 M NaCl). After the incubation, the reaction was treated with ¼ units of duplex specific nuclease (DSN). The normalized cDNA was then amplified from 1 µl of DSN-treated cDNA by PCR reactions (10 cycles) described above and gel purified for the fragment size of 400-800 bp as described above.454ESTTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLX ��double-haploid rainbow troutSRS004650 VTissues were collected from a single immature (~ 1-year-old) male double-haploid fish and frozen in liquid nitrogen and stored at -80C until total RNA isolation. Total RNA was isolated using TRIzol™ (Invitrogen, Carlsbad, CA) from fourteen tissues; white muscle, red muscle, testis, spleen, kidney, head kidney, pituitary, stomach, brain, heart, intestine, gill, skin, liver. Equal masses of total RNAs from various tissues were pooled and used to construct the 454 library.DTrout transcriptome-454SRP001007Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesOtherBackground: Rainbow trout is important fish species for aquaculture and biomedical research but has no genomic data. Until genome sequence becomes available, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Large-scale EST (258,973) Singer sequences are publicly available for rainbow trout. However, the nature of duplicated rainbow trout genome hinders assembly and annotation of the EST sequences. Additionally, previous efforts aimed at SNP discovery for rainbow trout using ESTs were unsuccessful, mainly, due to difficulties parsing allelic variation from the high frequency of duplicated genes. Results: High-throughput shotgun deep sequencing of the rainbow trout double-haploid transcriptome using DNA 454-pyrosequencing technology has been successfully applied yielding about 1.3 million reads with an average length of 344bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus sequences (TCs) (Average length 662 nt) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing Singer sequences resulted in 161,818 TCs (Average length 758 nt) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed similarity to the expected transcriptome of other fish species with known genome sequences, suggesting a genome-wide representation of the rainbow trout transcriptome sequence. Conclusion: The 454 library added great amount of new EST sequences and identified new genes. In addition, it improved assembly and annotation of the rainbow trout Sanger EST. The 454 library is a new tool for functional genome research in rainbow trout. It provides a reference sequence to identify gene duplications, allelic variations; distinguish true/false SNPs as well as for digital gene expression and proteomic research in rainbow trout.Oncorhynchus mykiss�YSRA009276West Virginia University,Animal Biotechnology and Genomics2009-08-052018-05-10 18:11:11
� � �p�S O ! �5 �Q �Y) �I! E E �] ; �Q�3 ?O!3��XRainbow trout transcriptome-454-2SRR0207402013-07-26
'X�v%�Rainbow trout transcriptome analysis using Sanger and 454-Pyrosequencing approachesSRX007396Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesMessenger RNA was isolated from total RNA using the Oligotex mRNA Mini kit (Qiagen, CA). First and second strand cDNA were synthesized from 200ng of mRNA using the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen, CA) with 100 µM random hexamer primers (Fermentas, USA). Double-stranded cDNA was cleaned up with a QIAquick Minelute PCR purification column (Qiagen, CA). Double-stranded DNA was nebulized with the nebulization kit supplied with the GS Titanium Library Preparation kit (Roche/454 Life Sciences, CT) following their recommendations (30psi for 1 minute) and cleaned up with a QIAquick PCR minelute column and eluted in 50ul EB. Nebulized cDNA was blunt-ended (25 µl water, 10 µl 10x T4 DNA Ligase buffer (NEB), 4 µl 10 mM dNTP mix, 5 µl T4 DNA polymerase (3 U/µl) (NEB), 1 µl Klenow polymerase (5 U/ µl) (NEB), and 5 µl Polynucleotide kinase (10 U/µl) (NEB) and cleaned up with a Qiaquick PCR minelute column and eluted in 32ul EB. A dA-overhang was added at 3’ end of cDNA by adding the following to the blunt-ended cDNA: 5 µl 10x buffer 2 (NEB), 10 µl 1 mM dATP and 3 µl Klenow exo-minus polymerase (5 U/µl) (NEB). The reaction was incubated at 370C for 30 minutes and then cleaned up with a QIAquick MiniElute column and eluted in 10 µl EB. The cDNA was adaptored with Titanium adaptors (Roche/454 Life Sciences, CT) by adding 9 µl water, 25 µl 2x Rapid Ligase buffer (Enzymatics, MA) 5 µl (50 µM) Titanium adapter A/B mix and 1 µl T4 DNA Ligase (600 U/µl (Enzymatics, MA) and incubated the ligation reaction at room temperature for 15 minutes. The reaction was cleaned up using a Qiaquick MiniElute column (Qiagen), eluting the cDNA in 20 µl EB. Adaptored cDNA was run on a E-GEL EX 2% agarose (Invitrogen, CA) following the manufacturer instructions and cDNAs in the size range of 400-800bp were excised from the gel and purified with a Qiagen’s Gel Extraction kit and the cDNA was eluted in 30 µl EB. One µl of the gel- purified cDNA was used as template for amplification in 50 µl PCR reactions containing 10 µl 5x Phusion Buffer HF (NEB), 25 µM Adapter A_For primer (5’CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGT3’), 25 µM Adapter B_For primer (5’CCTATCCCCTGTGTGCCTTGGCAGTCTCAGT3’), 3% DMSO, 10 mM dNTPs and 1 U Phusion polymerase (Finnzymes/NEB, USA). The PCR conditions were as follows: 980C for 30 seconds, followed by 15 cycles with 980C for 10 seconds, 680C for 30 seconds and 720C for 30 seconds, with a final extension of 720C for 5 minute and cleaned up with a Qiaquick minelute PCR column. Normalization of cDNA library The cDNA library was normalized according to the protocol described in the Trimmer Direct Kit (Evrogen, Russia). In brief, 300 ng of cDNA were incubated at 950C for 5 minutes followed by incubation at 680C for 4 hours in the hybridization buffer included in the kit (50 mM Hepes, pH7.5 and 0.5 M NaCl). After the incubation, the reaction was treated with ¼ units of duplex specific nuclease (DSN). The normalized cDNA was then amplified from 1 µl of DSN-treated cDNA by PCR reactions (10 cycles) described above and gel purified for the fragment size of 400-800 bp as described above.454ESTTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLX ��double-haploid rainbow troutSRS004650 VTissues were collected from a single immature (~ 1-year-old) male double-haploid fish and frozen in liquid nitrogen and stored at -80C until total RNA isolation. Total RNA was isolated using TRIzol™ (Invitrogen, Carlsbad, CA) from fourteen tissues; white muscle, red muscle, testis, spleen, kidney, head kidney, pituitary, stomach, brain, heart, intestine, gill, skin, liver. Equal masses of total RNAs from various tissues were pooled and used to construct the 454 library.DTrout transcriptome-454SRP001007Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesOtherBackground: Rainbow trout is important fish species for aquaculture and biomedical research but has no genomic data. Until genome sequence becomes available, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Large-scale EST (258,973) Singer sequences are publicly available for rainbow trout. However, the nature of duplicated rainbow trout genome hinders assembly and annotation of the EST sequences. Additionally, previous efforts aimed at SNP discovery for rainbow trout using ESTs were unsuccessful, mainly, due to difficulties parsing allelic variation from the high frequency of duplicated genes. Results: High-throughput shotgun deep sequencing of the rainbow trout double-haploid transcriptome using DNA 454-pyrosequencing technology has been successfully applied yielding about 1.3 million reads with an average length of 344bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus sequences (TCs) (Average length 662 nt) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing Singer sequences resulted in 161,818 TCs (Average length 758 nt) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed similarity to the expected transcriptome of other fish species with known genome sequences, suggesting a genome-wide representation of the rainbow trout transcriptome sequence. Conclusion: The 454 library added great amount of new EST sequences and identified new genes. In addition, it improved assembly and annotation of the rainbow trout Sanger EST. The 454 library is a new tool for functional genome research in rainbow trout. It provides a reference sequence to identify gene duplications, allelic variations; distinguish true/false SNPs as well as for digital gene expression and proteomic research in rainbow trout.Oncorhynchus mykiss�YSRA009276West Virginia University,Animal Biotechnology and Genomics2009-08-052018-05-10 18:11:11
U �U �+� O U! ! !K ? ) 3 W ! �-# e�W �o 3>�7w@14710B-3_L8_I20010.R1.clean.fastq.gzSRR59646222017-08-24 ��| � @�1a*14710B-3SRX3122356RNA-seq for MCF-7 breast cancerβ-estradiol_treat114710B-3RNA-SeqTRANSCRIPTOMICPCRPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,�14710B-3SRS2456862%�isolate: treat1 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human��PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism. HMSRA602313National Research Institute for Health and Family PlanningNational Research Institute for Health and Family2018-05-10 18:11:11�p�S O ! �5 �Q �Y) �I! E E �] ; �Q�3 ?O!3��WRainbow trout transcriptome-454-1SRR0207392013-07-26 �!%�Rainbow trout transcriptome analysis using Sanger and 454-Pyrosequencing approachesSRX007396Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesMessenger RNA was isolated from total RNA using the Oligotex mRNA Mini kit (Qiagen, CA). First and second strand cDNA were synthesized from 200ng of mRNA using the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen, CA) with 100 µM random hexamer primers (Fermentas, USA). Double-stranded cDNA was cleaned up with a QIAquick Minelute PCR purification column (Qiagen, CA). Double-stranded DNA was nebulized with the nebulization kit supplied with the GS Titanium Library Preparation kit (Roche/454 Life Sciences, CT) following their recommendations (30psi for 1 minute) and cleaned up with a QIAquick PCR minelute column and eluted in 50ul EB. Nebulized cDNA was blunt-ended (25 µl water, 10 µl 10x T4 DNA Ligase buffer (NEB), 4 µl 10 mM dNTP mix, 5 µl T4 DNA polymerase (3 U/µl) (NEB), 1 µl Klenow polymerase (5 U/ µl) (NEB), and 5 µl Polynucleotide kinase (10 U/µl) (NEB) and cleaned up with a Qiaquick PCR minelute column and eluted in 32ul EB. A dA-overhang was added at 3’ end of cDNA by adding the following to the blunt-ended cDNA: 5 µl 10x buffer 2 (NEB), 10 µl 1 mM dATP and 3 µl Klenow exo-minus polymerase (5 U/µl) (NEB). The reaction was incubated at 370C for 30 minutes and then cleaned up with a QIAquick MiniElute column and eluted in 10 µl EB. The cDNA was adaptored with Titanium adaptors (Roche/454 Life Sciences, CT) by adding 9 µl water, 25 µl 2x Rapid Ligase buffer (Enzymatics, MA) 5 µl (50 µM) Titanium adapter A/B mix and 1 µl T4 DNA Ligase (600 U/µl (Enzymatics, MA) and incubated the ligation reaction at room temperature for 15 minutes. The reaction was cleaned up using a Qiaquick MiniElute column (Qiagen), eluting the cDNA in 20 µl EB. Adaptored cDNA was run on a E-GEL EX 2% agarose (Invitrogen, CA) following the manufacturer instructions and cDNAs in the size range of 400-800bp were excised from the gel and purified with a Qiagen’s Gel Extraction kit and the cDNA was eluted in 30 µl EB. One µl of the gel- purified cDNA was used as template for amplification in 50 µl PCR reactions containing 10 µl 5x Phusion Buffer HF (NEB), 25 µM
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ѯisolate: 770444.001 || cultivar: Camansi || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�� O U! ! !K ) 3 W ! �1# e�W �o 3>��7wA14710B-2_L8_I20009.R2.clean.fastq.gzSRR59646232017-08-24 �yix��1a)14710B-2SRX3122355RNA-seq for MCF-7 breast cancercontrol214710B-2RNA-SeqTRANSCRIPTOMICPCRPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,�14710B-2SRS2456861%�isolate: control2 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human��PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism. HMSRA602313National Research Institute for Health and Family PlanningNational Research Institute for Health and Family2018-05-10 18:11:11�+� O U! ! !K ? ) 3 W ! �-# e�W �o 3>��7w?14710B-4_L8_I20011.R1.clean.fastq.gzSRR59646212017-08-24 Dzo �f�1a+14710B-4SRX3122357RNA-seq for MCF-7 breast cancerβ-estradiol_treat214710B-4RNA-SeqTRANSCRIPTOMICPCRPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,�14710B-4SRS2456864%�isolate: treat2 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human��PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism. HMSRA602313National Research Institute for Health and Family PlanningNational Research Institute for Health and Family2018-05-10 18:11:11� �
O U! ! !K ) 3 W ! �1# e�W �o 3>��7wB14710B-1_L8_I20008.R2.clean.fastq.gzSRR59646242017-08-24 �av ��$01a(14710B-1SRX3122354RNA-seq for MCF-7 breast cancercontrol114710B-1RNA-SeqTRANSCRIPTOMICPCRPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,�14710B-1SRS2456863%�isolate: control1 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human��PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism. HMSRA602313National Research Institute for Health and Family PlanningNational Research Institute for Health and Family2018-05-10 18:11:11
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%R �O�P /! ! !Q �) 3 W ! �# � �! ;_ 3>��8]RNA24_R2.fastq.gzSRR59975242017-09-01/�� �:�1��RNA24SRX3153048RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA24RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA24SRS2484902��isolate: 900261.001 || cultivar: Samoan 2 || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�W�P /! ! !Y �) 3 W ! � # � �! ;_ 3>��8eRNA34_R2.fastq.gzSRR59975322017-09-01��� 6�QH1��RNA34SRX3153040RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA34RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA34SRS2484894
ѯisolate: 890455.001 || cultivar: Ulu fatu || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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ѯisolate: 389.001 || cultivar: Kapiak || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�h�Q /! ! !� �) 3 W ! �# � �! ;_ 3>��8`RNA48_R1.fastq.gzSRR59975272017-09-01 ��� ���1��RNA48SRX3153045RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA48RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA48SRS2484899Z�isolate: 890184.001 || cultivar: Luthar || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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&: �h�Q /! ! !� �) 3 W ! �# � �! ;_ 3>��8\RNA10_R2.fastq.gzSRR59975232017-09-01F� ס�d1��RNA10SRX3153049RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA10RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA10SRS2484903Z�isolate: 790490.001 || cultivar: Rotuma || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�V�P /! ! !Y �) 3 W ! �# � �! ;_ 3>��8gRNA37_R2.fastq.gzSRR59975342017-09-01
� ��L�1��RNA37SRX3153038RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA37RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA37SRS2484892
ѯisolate: 980212.001 || cultivar: Camansi || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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5 �U�P /! ! !Y �) 3 W ! �# � �! ;_ 3>��8^RNA21_R2.fastq.gzSRR59975252017-09-01m� �)N1��RNA21SRX3153047RNA-Seq of Artocarpus altilis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA21RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA21SRS2484901��isolate: 900265.001 || cultivar: Karawa || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�n�Q /! ! !� �) 3 W ! � # � �! ;_ 3>��8WRNA17_R1.fastq.gzSRR59975182017-09-01 �Qq ��C*1��RNA17SRX3153054RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA17RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA17SRS2484908Z�isolate: 790487.001 || cultivar: Unk (Huehue) || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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/a �J�P +! ! !Y �) 3 W ! �# � �! ;_ 3>��8cEW2_R2.fastq.gzSRR59975302017-09-01_�� q�1��EW2SRX3153042RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingEW2RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��EW2SRS2484896
ѯisolate: 501.005 || cultivar: Kapiak || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�M�P /! ! !Q �) 3 W ! �# � �! ;_ 3>��8lRNA49_R2.fastq.gzSRR59975392017-09-01 �� ���1��RNA49SRX3153033RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA49RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA49SRS2484887��isolate: 910265.001 || cultivar: Rotuma || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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J �N�P /! ! !Q �) 3 W ! �# � �! ;_ 3>��8URNA26_R2.fastq.gzSRR59975162017-09-01 �� ����1��RNA26SRX3153056RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA26RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,�RNA26SRS2484910��isolate: 890167.002 || cultivar: Meisaip || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�`�P +! ! !q �) 3 W ! �'# � �! ;_ 3>��8bEW4_R1.fastq.gzSRR59975292017-09-01�7� VHd1��EW4SRX3153043RNA-Seq of Artocarpus camansi root, stem, and leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingEW4RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��EW4SRS2484897
ѯisolate: 501 || cultivar: Kapiak || dev_stage: Seedling || geo_loc_name: USA: Hawaii || tissue: Root, Stem, and Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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0Z �R�P -! ! !Y �) 3 W ! �# � �! ;_ 3>��8hRNA2_R1.fastq.gzSRR59975352017-09-01 �� ���1��RNA2SRX3153037RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA2RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA2SRS2484891
ѯisolate: 910280.001 || cultivar: Meikole || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�L�P +! ! !Y �) 3 W ! �# � �! ;_ 3>��8jEW3_R2.fastq.gzSRR59975372017-09-01w�j (KS�1��EW3SRX3153035RNA-Seq of Artocarpus altilis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingEW3RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��EW3SRS2484889��isolate: 30042.001 || cultivar: Toneno || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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&U �M� P /! ! !Q �) 3 W ! �# � �! ;_ 3>��8VRNA25_R1.fastq.gzSRR59975172017-09-01�C Γ��1��RNA25SRX3153055RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA25RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,� RNA25SRS2484909��isolate: 890479.002 || cultivar: Meisei || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�V� P -! ! !c �) 3 W ! �# � �! ;_ 3>��8dRNA7_R1.fastq.gzSRR59975312017-09-01 ڐD �uը1��RNA7SRX3153041RNA-Seq of Artocarpus mariannensis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA7RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA7SRS2484895
Ѽisolate: 900252.002 || cultivar: Dugdug || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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2J �d� Q /! ! !� �) 3 W ! �# � �! ;_ 3>��8XRNA40_R1.fastq.gzSRR59975192017-09-01gj�Q�5�1��RNA40SRX3153053RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA40RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA40SRS2484907Z�isolate: 910269.001 || cultivar: Faine || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�J� P /! ! !Q �) 3 W ! � # � �! ;_ 3>��8iRNA38_R1.fastq.gzSRR59975362017-09-01de� 8K�1��RNA38SRX3153036RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA38RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA38SRS2484890��isolate: 880690.001 || cultivar: Kea || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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�) 3 W ! �'# � �! ;_ 3>��8YRNA36_R2.fastq.gzSRR59975202017-09-01 ��;k ��1��RNA36SRX3153052RNA-Seq of Artocarpus altilis x Artocarpus mariannensis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA36RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA36SRS2484906Z�isolate: 890173.002 || cultivar: Ulu afa elise || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�q� Q /! ! !�
�) 3 W ! �# � �! ;_ 3>��8ZRNA32_R1.fastq.gzSRR59975212017-09-01&({ ��1��RNA32SRX3153051RNA-Seq of Artocarpus altilis x Artocarpus mariannensis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA32RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA32SRS2484905Z�isolate: 890174.001 || cultivar: Ulu afa || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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/B �i�#Q /! ! !� �) 3 W ! �# � �! ;_ 3>��8_RNA16_R2.fastq.gzSRR59975262017-09-01fs ~��1��RNA16SRX3153046RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA16RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA16SRS2484900Z�isolate: 890183.001 || cultivar: Midolab || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�M�"P /! ! !Q �) 3 W ! �# � �! ;_ 3>��8kRNA39_R1.fastq.gzSRR59975382017-09-01=~( ����1��RNA39SRX3153034RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA39RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��RNA39SRS2484888��isolate: 790485.001 || cultivar: Puupuu || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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D3SRX3153086diploid tumor 3DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D3WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�D3SRS2484936%�isolate: breast cancer patient from Sweden || age: 45 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11�K�$P +! ! !Y �) 3 W ! �# � �! ;_ 3>��8[EW1_R2.fastq.gzSRR59975222017-09-01SK �7x1��EW1SRX3153050RNA-Seq of Artocarpus altilis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingEW1RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000,��EW1SRS2484904��isolate: 970236 || cultivar: Ulu fiti || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant�yPRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.Artocarpus TSRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
� � �{�&P {! ! !/ �{- # G ! �q# �1;�7% ? 3>��8�GTTTCG_1_3_000000000-ADYRF.750_BUSTARD-2015-06-23.fq.gzSRR59975692017-09-01�� �CV1�A5SRX3153077aneuploid tumor 5DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A5WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�A5SRS2484927%�isolate: breast cancer patient from Sweden || age: 64 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
� � �q�'P q! ! !+ �{- # G ! �q# �1;�7% ? 3>��8�ACTGAT_X_1_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975662017-09-01iY}97��1�D5SRX3153080diploid tumor 5DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D5WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�D5SRS2484930%�isolate: breast cancer patient from Sweden || age: 69 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
� � �{�(P {! ! !/ �{- # G ! �q# �1;�7% ? 3>�8�GTGGCC_1_3_000000000-ADYRF.750_BUSTARD-2015-06-23.fq.gzSRR59975672017-09-01]�� �(��1�A1SRX3153079aneuploid tumor 1DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A1WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�A1SRS2484929%�isolate: breast cancer patient from Sweden || age: 40 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
q q � �)P {! ! !/ �{- # G ! �# �1;�7% ? 3>�8�ATGTCA_1_1_000000000-ADYRF.750_BUSTARD-2015-06-23.fq.gzSRR59975652017-09-01e~� ��"�1�A3SRX3153081aneuploid tumor 3DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A3WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�A3SRS2484931%�isolate: breast cancer patient from Sweden || age: 53 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
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v)��1� D4SRX3153085diploid tumor 4DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D4WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�D4SRS2484935%�isolate: breast cancer patient from Sweden || age: 62 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
y y ��+P q! ! !/ �{- # G ! �# �1;�7% ? 3>�8�GTCCGC_X_3_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975642017-09-01ll�:��1�A2SRX3153082aneuploid tumor 2DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A2WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�A2SRS2484932%�isolate: breast cancer patient from Sweden || age: 60 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
t t ��,P q! ! !+ �{- # G ! �# �1;�7% ? 3>�8�ATTCCT_X_1_AH3KYTAFXX.811_NEXTSEQ-2015-09-04.fq.gzSRR59975632017-09-01E w 8� �1�D2SRX3153083diploid tumor 2DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D2WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�D2SRS2484934%�isolate: breast cancer patient from Sweden || age: 72 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead not by breast cancer || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
y y ��-P q! ! !/ �{- # G ! �# �1;�7% ? 3>�8�ATCACG_X_3_AH3KYTAFXX.811_NEXTSEQ-2015-09-04.fq.gzSRR59975702017-09-01`�>5C�1� A6SRX3153076aneuploid tumor 6DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A6WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�A6SRS2484926%�isolate: breast cancer patient from Sweden || age: 46 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
� � �t�.P q! ! !+ �{- # G ! �q# �1;�7% ? 3>�8�TTAGGC_X_1_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975622017-09-01D΅ ��s1�D1SRX3153084diploid tumor 1DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D1WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�D1SRS2484933%�isolate: breast cancer patient from Sweden || age: 66 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
1 x1 �C�0Q '! ! ! !!� ) �7 3 W !! �g �?9�# A 3?|7: _GSM2791401_r1SRR60677392017-10-11=n� �z�GSM27914013� GSM2791401SRX3209941GSM2791401: HBCx-22 PDX treated with vehicle #3; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500-��GSM2791401SRS2534923%�source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveʻGSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177 ��SRA612572submission brokered by GEOGEO2018-05-10 18:11:11��/P q! ! !/ �{- # G ! �# �1;�7% ? 3>�8�GTGAAA_X_1_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975682017-09-01 �w|(Y1�A4SRX3153078aneuploid tumor 4DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A4WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500,�A4SRS2484928%�isolate: breast cancer patient from Sweden || age: 49 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: Human�|PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiens TSRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
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� �L[�GSM27914043�GSM2791404SRX3209944GSM2791404: HBCx-22 PDX treated with RAD140 #6; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500-��GSM2791404SRS2534926%�source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveʻGSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177 ��SRA612572submission brokered by GEOGEO2018-05-10 18:11:11�C�1Q '! ! ! !!� ) �7 3 W !! �g �?9�# A 3?|8: ^GSM2791400_r1SRR60677382017-10-11F� �xC�GSM27914003�GSM2791400SRX3209940GSM2791400: HBCx-22 PDX treated with vehicle #2; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500-��GSM2791400SRS2534922%�source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveʻGSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177 ��SRA612572submission brokered by GEOGEO2018-05-10 18:11:11
t �t �A�4Q '! ! ! !!� ) �7 3 W !! �e �?9�# A 3?|;: `GSM2791402_r1SRR60677402017-10-11@ % �־GSM27914023�GSM2791402SRX3209942GSM2791402: HBCx-22 PDX treated with RAD140 #4; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500-��GSM2791402SRS2534925%�source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveʻGSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177 ��SRA612572submission brokered by GEOGEO2018-05-10 18:11:11�C�3Q '! ! ! !!� ) �7 3 W !! �g �?9�# A 3?|:: ]GSM2791399_r1SRR60677372017-10-11� �$?bGSM27913993�GSM2791399SRX3209939GSM2791399: HBCx-22 PDX treated with vehicle #1; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500-��GSM2791399SRS2534921%�source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveʻGSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177 ��SRA612572submission brokered by GEOGEO2018-05-10 18:11:11
� � �A�5Q '! ! ! !!� ) �7 3 W !! �e �?9�# A 3?|<: aGSM2791403_r1SRR60677412017-10-11D�? �t�GSM27914033�GSM2791403SRX3209943GSM2791403: HBCx-22 PDX treated with RAD140 #5; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500-��GSM2791403SRS2534924%�source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positiveʻGSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177 ��SRA612572submission brokered by GEOGEO2018-05-10 18:11:11
� � ��6P '! ! ! !!g ) �{ 3 W ?!! �= �K9�) A 3?|�: gGSM2791564_r1SRR60688782017-10-11M�� ^�hGSM27915643�GSM2791564SRX3210847GSM2791564: 37NormPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791564-�GSM2791564SRS2535694%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O101 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �7P '! ! ! !!i ) �{ 3 W ?!! �I �K9�) A 3?|�: }GSM2791586_r1SRR60689002017-10-11Vv� cV��GSM27915863� GSM2791586SRX3210869GSM2791586: 83NPP_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791586-�(GSM2791586SRS2535716%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: U784 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �!�8P '! ! ! !!g ) �{ 3 W ?!! �O �K9�) A 3?|�: zGSM2791583_r1SRR60688972017-10-11 º A��pGSM27915833�GSM2791583SRX3210866GSM2791583: 68HPP_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791583-�%GSM2791583SRS2535713%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: U781 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �9P '! ! ! !!i ) �{ 3 W ?!! �I �K9�) A 3?|�: uGSM2791578_r1SRR60688922017-10-11Q7 `8� GSM27915783�GSM2791578SRX3210861GSM2791578: 67NPP_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791578-� GSM2791578SRS2535708%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: U776 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��:P '! ! ! !!g ) �{ 3 W ?!! �3 �K9�) A 3?|�: dGSM2791561_r1SRR60688752017-10-11�Tk � �GSM27915613�GSM2791561SRX3210844GSM2791561: 38HipTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791561-�GSM2791561SRS2535691%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Total mRNA || barcode: O098 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �;P '! ! ! !!i ) �{ 3 W ?!! �G �K9�) A 3?|�: rGSM2791575_r1SRR60688892017-10-11�1� � ��GSM27915753�GSM2791575SRX3210858GSM2791575: 44HipPPPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791575-� GSM2791575SRS2535705%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: O112 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �<P '! ! ! !!m ) �{ 3 W ?!! �A �K9�) A 3?|�: mGSM2791570_r1SRR60688842017-10-11/ 2{�GSM27915703�GSM2791570SRX3210853GSM2791570: 43NormPPTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791570-�GSM2791570SRS2535699%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: O107 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �=P '! ! ! !!m ) �{ 3 W ?!! �A �K9�) A 3?} : eGSM2791562_r1SRR60688762017-10-11W;` c�A GSM27915623�GSM2791562SRX3210845GSM2791562: 39NormPPTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791562-�GSM2791562SRS2535692%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: O099 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �"�>P '! ! ! !!g ) �{ 3 W ?!! �Q �K9�) A 3?}: yGSM2791582_r1SRR60688962017-10-11.o K`I�GSM27915823�GSM2791582SRX3210865GSM2791582: 67NPP_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791582-�$GSM2791582SRS2535712%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: U780 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �?P '! ! ! !!i ) �{ 3 W ?!! �G �K9�) A 3?}: vGSM2791579_r1SRR60688932017-10-11q{� sa�PGSM27915793�GSM2791579SRX3210862GSM2791579: 68HPP_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791579-�!GSM2791579SRS2535709%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: U777 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��@P '! ! ! !!e ) �{ 3 W ?!! �= �K9�) A 3?}: {GSM2791584_r1SRR60688982017-10-11= � �I��GSM27915843� GSM2791584SRX3210867GSM2791584: 81N_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791584-�&GSM2791584SRS2535714%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Total mRNA || barcode: U782 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��AP '! ! ! !!e ) �{ 3 W ?!! �; �K9�) A 3?}: |GSM2791585_r1SRR60688992017-10-11�� � �hGSM27915853� GSM2791585SRX3210868GSM2791585: 82H_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791585-�'GSM2791585SRS2535715%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Total mRNA || barcode: U783 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �BP '! ! ! !!k ) �{ 3 W ?!! �I �K9�) A 3?}: iGSM2791566_r1SRR60688802017-10-11o� q���GSM27915663�
GSM2791566SRX3210849GSM2791566: 39NormPPPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791566-�GSM2791566SRS2535696%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: O103 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��CP '! ! ! !!e ) �{ 3 W ?!! �; �K9�) A 3?}: hGSM2791565_r1SRR60688792017-10-11� ( GSM27915653� GSM2791565SRX3210848GSM2791565: 38HipPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791565-�GSM2791565SRS2535695%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: O102 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��DP '! ! ! !!e ) �{ 3 W ?!! �; �K9�) A 3?}: tGSM2791577_r1SRR60688912017-10-11j�� o>�GSM27915773�GSM2791577SRX3210860GSM2791577: 66H_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791577-� GSM2791577SRS2535707%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Total mRNA || barcode: U775 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��EP '! ! ! !!e ) �{ 3 W ?!! �= �K9�) A 3?}: sGSM2791576_r1SRR60688902017-10-11ֈ� aOGSM27915763�GSM2791576SRX3210859GSM2791576: 65N_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791576-� GSM2791576SRS2535706%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Total mRNA || barcode: U774 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��FP '! ! ! !!c ) �{ 3 W ?!! �E �K9�) A 3?} : wGSM2791580_r1SRR60688942017-10-11�`{ �IGSM27915803�GSM2791580SRX3210863GSM2791580: 65N_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791580-�"GSM2791580SRS2535710%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Polysomal mRNA || barcode: U778 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
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: cGSM2791560_r1SRR60688742017-10-11_� hj��GSM27915603�GSM2791560SRX3210843GSM2791560: 37NormTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791560-�GSM2791560SRS2535690%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Total mRNA || barcode: O097 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��HP '! ! ! !!g ) �{ 3 W ?!! �3 �K9�) A 3?} : lGSM2791569_r1SRR60688832017-10-11��Q ��pGSM27915693�
GSM2791569SRX3210852GSM2791569: 42HipTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791569-�GSM2791569SRS2535700%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Total mRNA || barcode: O106 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��IP '! ! ! !!e ) �{ 3 W ?!! �; �K9�) A 3?} : pGSM2791573_r1SRR60688872017-10-11�� ���GSM27915733�GSM2791573SRX3210856GSM2791573: 42HipPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791573-�GSM2791573SRS2535703%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: O110 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
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: kGSM2791568_r1SRR60688822017-10-11�7 �ȭXGSM27915683� GSM2791568SRX3210851GSM2791568: 41NormTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791568-�GSM2791568SRS2535697%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Total mRNA || barcode: O105 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��KP '! ! ! !!g ) �{ 3 W ?!! �= �K9�) A 3?}: oGSM2791572_r1SRR60688862017-10-11� Ȝ'hGSM27915723�GSM2791572SRX3210855GSM2791572: 41NormPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791572-�GSM2791572SRS2535702%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O109 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �LP '! ! ! !!i ) �{ 3 W ?!! �G �K9�) A 3?}: jGSM2791567_r1SRR60688812017-10-11-ct J� �GSM27915673� GSM2791567SRX3210850GSM2791567: 40HipPPPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791567-�GSM2791567SRS2535698%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: O104 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��MP '! ! ! !!c ) �{ 3 W ?!! �C �K9�) A 3?}: �GSM2791589_r1SRR60689032017-10-11$� <���GSM27915893�!GSM2791589SRX3210872GSM2791589: 82H_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791589-�+GSM2791589SRS2535719%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: U787 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��NP '! ! ! !!c ) �{ 3 W ?!! �C �K9�) A 3?}: xGSM2791581_r1SRR60688952017-10-11�i1 �uGSM27915813�GSM2791581SRX3210864GSM2791581: 66H_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791581-�#GSM2791581SRS2535711%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: U779 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��OP '! ! ! !!c ) �{ 3 W ?!! �E �K9�) A 3?}: GSM2791588_r1SRR60689022017-10-11"6� DP��GSM27915883� GSM2791588SRX3210871GSM2791588: 81N_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791588-�*GSM2791588SRS2535718%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Polysomal mRNA || barcode: U786 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��PP '! ! ! !!k ) �{ 3 W ?!! �? �K9�) A 3?}: nGSM2791571_r1SRR60688852017-10-11[� f��GSM27915713�GSM2791571SRX3210854GSM2791571: 44HipPPTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791571-�GSM2791571SRS2535701%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: O108 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �!�QP '! ! ! !!g ) �{ 3 W ?!! �O �K9�) A 3?}: �GSM2791591_r1SRR60689052017-10-11�� �%�8GSM27915913�#GSM2791591SRX3210874GSM2791591: 84HPP_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791591-�-GSM2791591SRS2535721%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: U789 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � ��RP '! ! ! !!k ) �{ 3 W ?!! �? �K9�) A 3?}: fGSM2791563_r1SRR60688772017-10-11&S( F�_�GSM27915633�GSM2791563SRX3210846GSM2791563: 40HipPPTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791563-�GSM2791563SRS2535693%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: O100 || replicate: Biological replicate 1ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �SP '! ! ! !!i ) �{ 3 W ?!! �G �K9�) A 3?}: ~GSM2791587_r1SRR60689012017-10-11 8 :�!@GSM27915873� GSM2791587SRX3210870GSM2791587: 84HPP_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791587-�)GSM2791587SRS2535717%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: U785 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �"�TP '! ! ! !!g ) �{ 3 W ?!! �Q �K9�) A 3?}: �GSM2791590_r1SRR60689042017-10-11� ?N(�GSM27915903�"GSM2791590SRX3210873GSM2791590: 83NPP_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791590-�,GSM2791590SRS2535720%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: U788 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � � �UP '! ! ! !!k ) �{ 3 W ?!! �I �K9�) A 3?}: qGSM2791574_r1SRR60688882017-10-11�� {ǒGSM27915743�GSM2791574SRX3210857GSM2791574: 43NormPPPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791574-� GSM2791574SRS2535704%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: O111 || replicate: Biological replicate 2ʼGSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193 ��SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
Z� �&�XR #! ! !� �{- 3 W ! �# �M�A% � 51 3@�:A�Pat235C.bamSRR61174182017-10-16�� �N�X3�pPat235CSRX3230155Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat235COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.L Pat235CSRS2554666%�isolate: TEX_235_PrimTum || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�&�WR #! ! !� �{- 3 W ! �# �M�A% � 51 3@�:A�Pat170C.bamSRR61174202017-10-16�� CaX3�nPat170CSRX3230153Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat170COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.L Pat170CSRS2554664%�isolate: TEX_170_PrimTum || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�"�VR #! ! !� �{- 3 W ! �}# �M�A% � 51 3@�:A�Pat067N.bamSRR61174232017-10-16�PN μ�3�kPat067NSRX3230150Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat067NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat067NSRS2554662%�isolate: TEX_067_Norm || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
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� V�� �3�^R %! ! !� �{ - 3 W ! �# �M�A% � 51 3@�:A�Pat4005N.bamSRR61174282017-10-16�g� y)X3�fPat4005NSRX3230145Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4005NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat4005NSRS2554657%�isolate: Prospective_4005_ID8_Norm || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�7�]R %! ! !� �{ - 3 W ! � # �M�A% � 51 3@�:A�Pat4037C.bamSRR61174322017-10-16YA� ջ~3�bPat4037CSRX3230141Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4037COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.K�Pat4037CSRS2554653%�isolate: Prospective_4037_ID7_PrimTum || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�&�\R #! ! !� �{- 3 W ! �# �M�A% � 51 3@�:A�Pat224M.bamSRR61174242017-10-16�� � S�3�jPat224MSRX3230149Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat224MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat224MSRS2554661%�isolate: TEX_224_Met || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lymph node || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� I�� �4�aR %! ! !� �{ - 3 W ! �# �M�A% � 51 3@�:A�Pat4024M.bamSRR61174342017-10-16�� Um�3�`Pat4024MSRX3230139Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4024MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.K�Pat4024MSRS2554651%�isolate: Prospective_4024_ID19_Met || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�3�`R %! ! !� �{ - 3 W ! �# �M�A% � 51 3@�:A�Pat4037N.bamSRR61174362017-10-16`�� ۉ{P3�^Pat4037NSRX3230137Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4037NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.K�Pat4037NSRS2554649%�isolate: Prospective_4037_ID7_Norm || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�3�_R #! ! !� �{- 3 W ! � # �M�A% � 51 3@�:A�Pat059C.bamSRR61174112017-10-16&ߗ v^��3�wPat059CSRX3230162Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat059COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat059CSRS2554673%�isolate: TEX_059_PrimTum || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast (lymph node) || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
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Pat235MSRS2554665%�isolate: TEX_235_Met || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Skin || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�2�cR %! ! !� �{ - 3 W ! �# �M�A% � 51 3@�:A�Pat4005M.bamSRR61174292017-10-16$ �%x3�ePat4005MSRX3230144Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4005MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat4005MSRS2554656%�isolate: Prospective_4005_ID8_Met || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�4�bR %! ! !� �{ - 3 W ! �# �M�A% � 51 3@�:A�Pat4024N.bamSRR61174332017-10-16Q$� _d��3�aPat4024NSRX3230140Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4024NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.K�Pat4024NSRS2554652%�isolate: Prospective_4024_ID19_Norm || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
Z� �!�gR #! ! !� �{- 3 W ! �{# �M�A% � 51 3@�:A�Pat044M.bamSRR61174132017-10-16�� �W��3�uPat044MSRX3230160Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat044MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat044MSRS2554671%�isolate: TEX_044_Met || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�&�fR #! ! !� �{- 3 W ! �# �M�A% � 51 3@�:A�Pat066C.bamSRR61174142017-10-16�) :��3�tPat066CSRX3230159Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat066COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat066CSRS2554670%�isolate: TEX_066_PrimTum || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�"�eR #! ! !� �{- 3 W ! �}# �M�A% � 51 3@�:A�Pat235N.bamSRR61174312017-10-16�jw Mc,�3�cPat235NSRX3230142Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat235NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.K�Pat235NSRS2554654%�isolate: TEX_235_Norm || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
\� �!�jR #! ! !� �{- 3 W ! �{# �M�A% � 51 3@�:A�Pat170M.bamSRR61174212017-10-16�� �hP3�mPat170MSRX3230152Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat170MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat170MSRS2554663%�isolate: TEX_170_Met || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�"�iR #! ! !� �{- 3 W ! �}# �M�A% � 51 3@�:A�Pat059N.bamSRR61174172017-10-16&�` �n� 3�qPat059NSRX3230156Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat059NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.L Pat059NSRS2554667%�isolate: TEX_059_Norm || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11� �hR #! ! !� �{- 3 W ! �y# �M�A% � 51 3@�:A�Pat067M.bamSRR61174222017-10-16��{ ���3�lPat067MSRX3230151Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat067MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat067MSRS2554678%�isolate: TEX_067_Met || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lung || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� Z�� �3�mR #! ! !� �{- 3 W ! � # �M�A% � 51 3@�:A�Pat224C.bamSRR61174272017-10-16�� �e@3�gPat224CSRX3230146Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat224COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat224CSRS2554658%�isolate: TEX_224_PrimTum || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast (lymph node) || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�1�lR %! ! !� �{ - 3 W ! �# �M�A% � 51 3@�:A�Pat4037M.bamSRR61174372017-10-16~f, ��`3�]Pat4037MSRX3230136Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4037MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat4037MSRS2554677%�isolate: Prospective_4037_ID7_Met || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Bone || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�"�kR #! ! !� �{- 3 W ! �}# �M�A% � 51 3@�:A�Pat066N.bamSRR61174082017-10-16v�0 첝�3�zPat066NSRX3230165Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat066NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat066NSRS2554676%�isolate: TEX_066_Norm || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� Z�� �&�pR #! ! !� �{- 3 W ! �# �M�A% � 51 3@�:A�Pat059M.bamSRR61174162017-10-16u �2�h3�rPat059MSRX3230157Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat059MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.L
Pat059MSRS2554668%�isolate: TEX_059_Met || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lymph node || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�7�oR %! ! !� �{ - 3 W ! � # �M�A% � 51 3@�:A�Pat4005C.bamSRR61174302017-10-16F�� We��3�dPat4005CSRX3230143Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4005COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.L Pat4005CSRS2554655%�isolate: Prospective_4005_ID8_PrimTum || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�"�nR #! ! !� �{- 3 W ! �}# �M�A% � 51 3@�:A�Pat044N.bamSRR61174102017-10-16<�u ���h3�xPat044NSRX3230163Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat044NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat044NSRS2554674%�isolate: TEX_044_Norm || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� Z�� �!�sR #! ! !� �{- 3 W ! �{# �M�A% � 51 3@�:A�Pat066M.bamSRR61174152017-10-16zO& '�հ3�sPat066MSRX3230158Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat066MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat066MSRS2554669%�isolate: TEX_066_Met || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�8�rR %! ! !� �{ - 3 W ! �!# �M�A% � 51 3@�:A�Pat4024C.bamSRR61174352017-10-16��q US0H3�_Pat4024CSRX3230138Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4024COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.K�Pat4024CSRS2554650%�isolate: Prospective_4024_ID19_PrimTum || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�"�qR #! ! !� �{- 3 W ! �}# �M�A% � 51 3@�:A�Pat170N.bamSRR61174262017-10-16�� (S�3�hPat170NSRX3230147Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat170NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000.LPat170NSRS2554659%�isolate: TEX_179_Norm || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human��PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614 ��SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� � �~�tP '! ! ! !!�? ) �Y 3 W ?!! �e e�# A 3@`9: jGSM2806527_r1SRR61457732017-10-11%�-<�GSM28065273�!GSM2806527SRX3257822GSM2806527: IgG CLIP-seq in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500GEO Accession: GSM2806527. �GSM2806527SRS2571283%�source_name: BCBL-1 cells || infected with: Human gammaherpesvirus 8 || clip antibody: IgG (Sigma-Aldrich, Catalog Number I5381) || cell line: BCBL-1 || cell type: primary effusion lymphoma cell line which carries latently infected KSHV�GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GSE104711 ��SRA617783submission brokered by GEOGEO2018-05-10 18:11:11
� � �J�uP '! ! ! !!�A ) �Y 3 W ?!! �u e�# A 3@`:: kGSM2806528_r1SRR61457742017-10-11 � �w�.GSM28065283�"GSM2806528SRX3257823GSM2806528: K8 CLIP-seq-1 in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500GEO Accession: GSM2806528. �GSM2806528SRS2571284%�source_name: BCBL-1 cells || infected with: Human gammaherpesvirus 8 || clip antibody: K8 (generated and purified in our lab; Yan Wang, et al.,J Viral, 2011 and Xin Wang, et al., PLOS pathogens, 2015) || cell line: BCBL-1 || cell type: primary effusion lymphoma cell line which carries latently infected KSHV�GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GSE104711 ��SRA617783submission brokered by GEOGEO2018-05-10 18:11:11
� � �J�vP '! ! ! !!�A ) �Y 3 W ?!! �u e�# A 3@`;: lGSM2806529_r1SRR61457752017-10-11ݝ� �k(.GSM28065293�#GSM2806529SRX3257824GSM2806529: K8 CLIP-seq-2 in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeqâ„¢ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500GEO Accession: GSM2806529. �GSM2806529SRS2571285%�source_name: BCBL-1 cells || infected with: Human gammaherpesvirus 8 || clip antibody: K8 (generated and purified in our lab; Yan Wang, et al.,J Viral, 2011 and Xin Wang, et al., PLOS pathogens, 2015) || cell line: BCBL-1 || cell type: primary effusion lymphoma cell line which carries latently infected KSHV�GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GSE104711 ��SRA617783submission brokered by GEOGEO2018-05-10 18:11:11
# # �Y�wP '! ! ! !!� ) �Y 3 W ?!! �S e�# A 3@`<: mGSM2806530_r1SRR61457762017-10-114�n
$ GSM28065303�$GSM2806530SRX3257825GSM2806530: K8 CLIP-seq in BJAB cells; Homo sapiens; RIP-SeqGSE104711RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500GEO Accession: GSM2806530. �GSM2806530SRS2571286%�source_name: BJAB cells || clip antibody: K8 (generated and purified in our lab; Yan Wang, et al.,J Viral, 2011 and Xin Wang, et al., PLOS pathogens, 2015) || cell line: BJAB || cell type: KSHV-free Burkitt lymphoma B cell line�GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GSE104711 ��SRA617783submission brokered by GEOGEO2018-05-10 18:11:11
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�* �h�yP '! ! ! !!o ) �A 3 W ?!! � �E9�# A 3@bc: GSM2806581_r1SRR61470762017-10-11!�29���GSM28065813��GSM2806581SRX3259125GSM2806581: EtOH_11hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806581. �GSM2806581SRS2572558%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 11 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�f�xP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bb:
GSM2806577_r1SRR61470722017-10-11���M�r�GSM28065773��GSM2806577SRX3259121GSM2806577: EtOH_7hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806577. �GSM2806577SRS2572554%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 7 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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�, �f�{P '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@be: GSM2806571_r1SRR61470662017-10-11�bS��GSM28065713ϾGSM2806571SRX3259115GSM2806571: EtOH_1hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806571. �GSM2806571SRS2572548%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 1 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�f�zP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bd: GSM2806573_r1SRR61470682017-10-11m��H�0�GSM28065733�GSM2806573SRX3259117GSM2806573: EtOH_3hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806573. �GSM2806573SRS2572550%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 3 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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�& �j�}P '! ! ! !!m ) �A 3 W ?!! �% �E9�# A 3@bg: GSM2806570_r1SRR61470652017-10-11��OߡbGSM28065703ϽGSM2806570SRX3259114GSM2806570: DEX_11hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806570. �GSM2806570SRS2572547%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 11 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�h�|P '! ! ! !!o ) �A 3 W ?!! � �E9�# A 3@bf: GSM2806582_r1SRR61470772017-10-11T� Cֲ GSM28065823��GSM2806582SRX3259126GSM2806582: EtOH_11hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806582. �GSM2806582SRS2572559%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 11 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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�( �h�P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@bi: �GSM2806561_r1SRR61470562017-10-11j>�H*��GSM28065613ϴGSM2806561SRX3259105GSM2806561: DEX_3hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806561. wGSM2806561SRS2572538%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 3 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�h�~P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@bh: �GSM2806563_r1SRR61470582017-10-11Q\�C5|�GSM28065633϶GSM2806563SRX3259107GSM2806563: DEX_5hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806563. yGSM2806563SRS2572540%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 5 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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�( �f�P '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bk: GSM2806576_r1SRR61470712017-10-11�5W��GSM28065763��GSM2806576SRX3259120GSM2806576: EtOH_5hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806576. �GSM2806576SRS2572553%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 5 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�j� P '! ! ! !!m ) �A 3 W ?!! �% �E9�# A 3@bj: GSM2806569_r1SRR61470642017-10-11���Sc��GSM28065693ϼGSM2806569SRX3259113GSM2806569: DEX_11hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806569. GSM2806569SRS2572546%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 11 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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�( �h�P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@bm: �GSM2806560_r1SRR61470552017-10-11d�4 �GSM28065603ϳGSM2806560SRX3259104GSM2806560: DEX_1hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806560. vGSM2806560SRS2572537%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 1 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�h�P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@bl: GSM2806568_r1SRR61470632017-10-11���e���GSM28065683ϻGSM2806568SRX3259112GSM2806568: DEX_9hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806568. ~GSM2806568SRS2572545%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 9 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
,
�, �f�P '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bo: GSM2806575_r1SRR61470702017-10-11^ԮE�^�GSM28065753��GSM2806575SRX3259119GSM2806575: EtOH_5hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806575. �GSM2806575SRS2572552%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 5 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�f�P '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bn:
GSM2806574_r1SRR61470692017-10-11�H�WP��GSM28065743�GSM2806574SRX3259118GSM2806574: EtOH_3hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806574. �GSM2806574SRS2572551%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 3 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
*
�* �f�P '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bq: GSM2806572_r1SRR61470672017-10-11�]�c�tGSM28065723ϿGSM2806572SRX3259116GSM2806572: EtOH_1hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806572. �GSM2806572SRS2572549%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 1 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�h�P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@bp: GSM2806567_r1SRR61470622017-10-11�3���GSM28065673ϺGSM2806567SRX3259111GSM2806567: DEX_9hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806567. }GSM2806567SRS2572544%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 9 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
*
�* �f� P '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bs: GSM2806579_r1SRR61470742017-10-11��2Pu��GSM28065793��GSM2806579SRX3259123GSM2806579: EtOH_9hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806579. �GSM2806579SRS2572556%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 9 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�h�P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@br: GSM2806564_r1SRR61470592017-10-11_�E��GSM28065643ϷGSM2806564SRX3259108GSM2806564: DEX_5hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806564. zGSM2806564SRS2572541%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 5 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
*
�* �h� P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@bu: GSM2806565_r1SRR61470602017-10-11�NNQ�GSM28065653ϸGSM2806565SRX3259109GSM2806565: DEX_7hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806565. {GSM2806565SRS2572542%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 7 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�f�
P '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bt: GSM2806580_r1SRR61470752017-10-11iv�H�GSM28065803��GSM2806580SRX3259124GSM2806580: EtOH_9hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806580. �GSM2806580SRS2572557%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 9 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
*
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P '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3@bw: GSM2806578_r1SRR61470732017-10-11w��J��GSM28065783��GSM2806578SRX3259122GSM2806578: EtOH_7hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806578. �GSM2806578SRS2572555%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 7 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�h� P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@bv: GSM2806566_r1SRR61470612017-10-11(�D;#�GSM28065663ϹGSM2806566SRX3259110GSM2806566: DEX_7hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806566. |GSM2806566SRS2572543%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 7 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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�( �h�P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@by: �GSM2806559_r1SRR61470542017-10-11�%,M�g�GSM28065593ϲGSM2806559SRX3259103GSM2806559: DEX_1hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806559. uGSM2806559SRS2572536%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 1 hr || biological replicate: 1�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11�h�P '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3@bx: �GSM2806562_r1SRR61470572017-10-11�Z�SX�GSM28065623ϵGSM2806562SRX3259106GSM2806562: DEX_3hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806562. xGSM2806562SRS2572539%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 3 hr || biological replicate: 2�GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714 ��SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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u� ��P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c: wGSM2806596_r1SRR61479932017-10-11= /� GSM28065963�GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806596. �GSM2806596SRS2573349o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c: pGSM2806594_r2SRR61479862017-10-11= /� GSM28065943�GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806594. �GSM2806594SRS2573348o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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c� ��P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c: yGSM2806596_r3SRR61479952017-10-11= /� GSM28065963�GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806596. �GSM2806596SRS2573349o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c: `GSM2806590_r2SRR61479702017-10-11= /� GSM28065903�GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806590. �GSM2806590SRS2573344o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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u� ��P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c : xGSM2806596_r2SRR61479942017-10-11= /� GSM28065963�GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806596. �GSM2806596SRS2573349o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c: uGSM2806595_r3SRR61479912017-10-11= /� GSM28065953�GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806595. �GSM2806595SRS2573350o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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c� ��P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c : dGSM2806591_r2SRR61479742017-10-11= /� GSM28065913�GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806591. �GSM2806591SRS2573345o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c : eGSM2806591_r3SRR61479752017-10-11= /� GSM28065913�GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806591. �GSM2806591SRS2573345o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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u� ��P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c : fGSM2806591_r4SRR61479762017-10-11= /� GSM28065913�GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806591. �GSM2806591SRS2573345o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c : vGSM2806595_r4SRR61479922017-10-11= /� GSM28065953�GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806595. �GSM2806595SRS2573350o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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u� ��P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c": qGSM2806594_r3SRR61479872017-10-11= /� GSM28065943�GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806594. �GSM2806594SRS2573348o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c!: kGSM2806593_r1SRR61479812017-10-11= /� GSM28065933�GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806593. �GSM2806593SRS2573347o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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u� �� P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c$: aGSM2806590_r3SRR61479712017-10-11= /� GSM28065903�GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806590. �GSM2806590SRS2573344o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�� P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c#: sGSM2806595_r1SRR61479892017-10-11= /� GSM28065953�GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806595. �GSM2806595SRS2573350o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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u� �� P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c&: iGSM2806592_r3SRR61479792017-10-11= /� GSM28065923�GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806592. �GSM2806592SRS2573346o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�� P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c%: lGSM2806593_r2SRR61479822017-10-11= /� GSM28065933�GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806593. �GSM2806593SRS2573347o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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c� ��!P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c(: tGSM2806595_r2SRR61479902017-10-11= /� GSM28065953�GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806595. �GSM2806595SRS2573350o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�� P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c': hGSM2806592_r2SRR61479782017-10-11= /� GSM28065923�GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806592. �GSM2806592SRS2573346o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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c� ��#P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c*: mGSM2806593_r3SRR61479832017-10-11= /� GSM28065933�GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806593. �GSM2806593SRS2573347o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��"P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c): jGSM2806592_r4SRR61479802017-10-11= /� GSM28065923�GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806592. �GSM2806592SRS2573346o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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u� ��%P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c,: ^GSM2806589_r4SRR61479682017-10-11= /� GSM28065893�GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806589. �GSM2806589SRS2573343o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��$P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c+: rGSM2806594_r4SRR61479882017-10-11= /� GSM28065943�GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806594. �GSM2806594SRS2573348o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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u� ��'P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c.: oGSM2806594_r1SRR61479852017-10-11= /� GSM28065943�GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806594. �GSM2806594SRS2573348o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��&P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c-: nGSM2806593_r4SRR61479842017-10-11= /� GSM28065933�GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806593. �GSM2806593SRS2573347o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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c� ��)P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c0: cGSM2806591_r1SRR61479732017-10-11= /� GSM28065913�GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806591. �GSM2806591SRS2573345o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��(P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c/: ]GSM2806589_r3SRR61479672017-10-11= /� GSM28065893�GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806589. �GSM2806589SRS2573343o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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c� ��+P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c2: [GSM2806589_r1SRR61479652017-10-11= /� GSM28065893�GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806589. �GSM2806589SRS2573343o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��*P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c1: \GSM2806589_r2SRR61479662017-10-11= /� GSM28065893�GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806589. �GSM2806589SRS2573343o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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c� ��-P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3@c4: zGSM2806596_r4SRR61479962017-10-11= /� GSM28065963�GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806596. �GSM2806596SRS2573349o"source_name: Wild type || strain: K96243 || genotype: Wild type�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��,P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c3: _GSM2806590_r1SRR61479692017-10-11= /� GSM28065903�GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806590. �GSM2806590SRS2573344o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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c� ��/P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c6: bGSM2806590_r4SRR61479722017-10-11= /� GSM28065903�GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806590. �GSM2806590SRS2573344o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11��.P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3@c5: gGSM2806592_r1SRR61479772017-10-11= /� GSM28065923�GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806592. �GSM2806592SRS2573346o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant�GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716 ��SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
� �� ��1P '! ! ! !!u ) �; 3 W ?!! �- �%9� A 3@g: GSM2806691_r1SRR61487292017-10-11 ���#�3hGSM28066913ПGSM2806691SRX3260749GSM2806691: CD3/28+cGAMP_3h_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806691.!�GSM2806691SRS2574059'jsource_name: helper T cell_CD3/28+cGAMP_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 3hrs� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11��0P '! ! ! !!k ) �; 3 W ?!! � �%9� A 3@g: GSM2806692_r1SRR61487302017-10-11 �U&�E�GSM28066923РGSM2806692SRX3260750GSM2806692: CD3/28_24h_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806692.!�GSM2806692SRS2574060'jsource_name: helper T cell_CD3/28_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28 for 24hrs� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
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: �GSM2806686_r1SRR61487242017-10-11 ��U$EGSM28066863КGSM2806686SRX3260744GSM2806686: Naive CD4_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806686.!�GSM2806686SRS2574058'jsource_name: helper T cell_Naive CD4 || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: none (naïve)� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11��2P '! ! ! !!u ) �; 3 W ?!! �- �%9� A 3@g : �GSM2806690_r1SRR61487282017-10-11 ��b �.�GSM28066903ОGSM2806690SRX3260748GSM2806690: CD3/28+cGAMP_3h_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806690.!�GSM2806690SRS2574064'jsource_name: helper T cell_CD3/28+cGAMP_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 3hrs� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
� �� ��5P '! ! ! !!i ) �; 3 W ?!! � �%9� A 3@g : �GSM2806689_r1SRR61487272017-10-11kNB���GSM28066893НGSM2806689SRX3260747GSM2806689: CD3/28_3h_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806689.!�GSM2806689SRS2574057'jsource_name: helper T cell_CD3/28_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28 for 3hrs� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11��4P '! ! ! !!w ) �; 3 W ?!! �1 �%9� A 3@g : GSM2806694_r1SRR61487322017-10-11 �(X0t��GSM28066943ТGSM2806694SRX3260752GSM2806694: CD3/28+cGAMP_24h_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806694.!�GSM2806694SRS2574062'jsource_name: helper T cell_CD3/28+cGAMP_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 24hrs� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
� �� ��7P '! ! ! !!i ) �; 3 W ?!! � �%9� A 3@g: �GSM2806687_r1SRR61487252017-10-11���I�m�GSM28066873ЛGSM2806687SRX3260745GSM2806687: Naive CD4_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806687.!�GSM2806687SRS2574056'jsource_name: helper T cell_Naive CD4 || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: none (naïve)� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11��6P '! ! ! !!w ) �; 3 W ?!! �1 �%9� A 3@g
: GSM2806695_r1SRR61487332017-10-11 ���$J��GSM28066953УGSM2806695SRX3260753GSM2806695: CD3/28+cGAMP_24h_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806695.!�GSM2806695SRS2574063'jsource_name: helper T cell_CD3/28+cGAMP_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 24hrs� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
� �� ��9P '! ! ! !!k ) �; 3 W ?!! � �%9� A 3@g: GSM2806693_r1SRR61487312017-10-11 �R �WGSM28066933СGSM2806693SRX3260751GSM2806693: CD3/28_24h_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806693.!�GSM2806693SRS2574061'jsource_name: helper T cell_CD3/28_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28 for 24hrs� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11��8P '! ! ! !!i ) �; 3 W ?!! � �%9� A 3@g: �GSM2806688_r1SRR61487262017-10-11 ��� NϵGSM28066883МGSM2806688SRX3260746GSM2806688: CD3/28_3h_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806688.!�GSM2806688SRS2574055'jsource_name: helper T cell_CD3/28_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28 for 3hrs� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725 ��SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
^ �^ �M�;P '! ! ! !!w ) �g 3 W ?!! � �9� A 3@i|: �GSM2806883_r1SRR61503672017-10-11�qY @;��GSM28068833�dGSM2806883SRX3262385GSM2806883: Liver - TCPOBOP K8; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806883."�GSM2806883SRS2575313'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11�M�:P '! ! ! !!w ) �g 3 W ?!! � �9� A 3@i{: �GSM2806884_r1SRR61503682017-10-11��� 3��`GSM28068843�eGSM2806884SRX3262386GSM2806884: Liver - TCPOBOP K9; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806884."�GSM2806884SRS2575314'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
Z �Z �O�=P '! ! ! !!{ ) �g 3 W ?!! � �9� A 3@i~: �GSM2806877_r1SRR61503612017-10-11�@G 6A1�GSM28068773�^GSM2806877SRX3262379GSM2806877: Liver - Corn Oil KS2; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806877."�GSM2806877SRS2575307'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11�O�<P '! ! ! !!{ ) �g 3 W ?!! � �9� A 3@i}: �GSM2806878_r1SRR61503622017-10-11�; DM��GSM28068783�_GSM2806878SRX3262380GSM2806878: Liver - Corn Oil KS3; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806878."�GSM2806878SRS2575308'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
d �d �J�?P '! ! ! !!q ) �g 3 W ?!! � �9� A 3@i�: �GSM2806881_r1SRR61503652017-10-11��� $�� GSM28068813�bGSM2806881SRX3262383GSM2806881: Liver - PCN KS6; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806881."�GSM2806881SRS2575311'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11�J�>P '! ! ! !!q ) �g 3 W ?!! � �9� A 3@i: �GSM2806879_r1SRR61503632017-10-11
� o��HGSM28068793�`GSM2806879SRX3262381GSM2806879: Liver - PCN KS4; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806879."�GSM2806879SRS2575309'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
a �a �J�AP '! ! ! !!q ) �g 3 W ?!! � �9� A 3@i�: �GSM2806880_r1SRR61503642017-10-11� ](�LGSM28068803�aGSM2806880SRX3262382GSM2806880: Liver - PCN KS5; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806880."�GSM2806880SRS2575310'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11�M�@P '! ! ! !!w ) �g 3 W ?!! � �9� A 3@i�: �GSM2806882_r1SRR61503662017-10-11�W^ "�nGSM28068823�cGSM2806882SRX3262384GSM2806882: Liver - TCPOBOP K7; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806882."�GSM2806882SRS2575312'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
� � �O�BP '! ! ! !!{ ) �g 3 W ?!! � �9� A 3@i�: �GSM2806876_r1SRR61503602017-10-11k � �D�GSM28068763�]GSM2806876SRX3262378GSM2806876: Liver - Corn Oil KS1; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806876."�GSM2806876SRS2575306'jsource_name: Liver || strain: C57BL/6 || genotype: wild type�
GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734 ��SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
Y Y �#�CP '! ! ! !! ) �1 3 W ?!! � �9�m A 3@i�: �GSM2806924_r1SRR61504152017-10-11 ��4�
GSM28069243�fGSM2806924SRX3262427GSM2806924: ATCC27064; Streptomyces clavuligerus; RNA-SeqGSE104738RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806924."�GSM2806924SRS2575351�wsource_name: mycelium || phenotype: wildtype || strain: ATCC 27064 || type-material: type strain of Streptomyces clavuligerus�GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGSE104738 ��SRA617916submission brokered by GEOGEO2018-05-10 18:11:11
� � �h�DP '! ! ! !!y ) �1 3 W ?!! � �9�m A 3@i�: �GSM2806925_r2SRR61504182017-10-11x�//(�GSM28069253�gGSM2806925SRX3262428GSM2806925: F613-1; Streptomyces clavuligerus; RNA-SeqGSE104738RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806925."�GSM2806925SRS2575352msource_name: mycelium || phenotype: industrial strain || strain: F613-1�GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGSE104738 ��SRA617916submission brokered by GEOGEO2018-05-10 18:11:11
Y Y �#�EP '! ! ! !! ) �1 3 W ?!! � �9�m A 3@i�: �GSM2806924_r2SRR61504162017-10-11 ��4���GSM28069243�fGSM2806924SRX3262427GSM2806924: ATCC27064; Streptomyces clavuligerus; RNA-SeqGSE104738RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806924."�GSM2806924SRS2575351�wsource_name: mycelium || phenotype: wildtype || strain: ATCC 27064 || type-material: type strain of Streptomyces clavuligerus�GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGSE104738 ��SRA617916submission brokered by GEOGEO2018-05-10 18:11:11
� � �h�FP '! ! ! !!y ) �1 3 W ?!! � �9�m A 3@i�: �GSM2806925_r1SRR61504172017-10-11x�//3�GSM28069253�gGSM2806925SRX3262428GSM2806925: F613-1; Streptomyces clavuligerus; RNA-SeqGSE104738RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806925."�GSM2806925SRS2575352msource_name: mycelium || phenotype: industrial strain || strain: F613-1�GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGSE104738 ��SRA617916submission brokered by GEOGEO2018-05-10 18:11:11
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� �+ �G 3@�;��SRR62140602017-10-25��� 5^WSRX3322823!� ENCODE biosample ENCBS195LAYSRS1860811%�Homo sapiens MCF-7 immortalized cell lineENCBS195LAY at ENCODE: https://www.encodeproject.org/ENCBS195LAY/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdfdev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder �JSRA6241032018-05-10 18:11:11� �GQ ! ! ! ! � #�
� �+ �G 3@�;��SRR62140592017-10-25ժ� <���5^VSRX3322822/z%SRS2627513 �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder �JSRA6241032018-05-10 18:11:11
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� �+ �G 3@��;� SRR62141072017-10-25A�� ���5^�SRX3322868!ӖENCODE biosample ENCBS200IWRSRS1860706%�Homo sapiens MCF-7 immortalized cell lineENCBS200IWR at ENCODE: https://www.encodeproject.org/ENCBS200IWR/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder �jSRA6241352018-05-10 18:11:11
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� �+ �G 3@��;�!SRR62141082017-10-25�t� �jL5^�SRX3322869!�0ENCODE biosample ENCBS488MMMSRS1860859%�Homo sapiens MCF-7 immortalized cell lineENCBS488MMM at ENCODE: https://www.encodeproject.org/ENCBS488MMM/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7 �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder �jSRA6241352018-05-10 18:11:11
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� �+ �G 3@� ;�cSRR62141962017-10-252�+ �
5�5^�SRX3322943!ӖENCODE biosample ENCBS200IWRSRS1860706%�Homo sapiens MCF-7 immortalized cell lineENCBS200IWR at ENCODE: https://www.encodeproject.org/ENCBS200IWR/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder ČSRA6241702018-05-10 18:11:11
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;�bSRR62141952017-10-25��7 �}�f5^�SRX3322942!ӈENCODE biosample ENCBS609QTYSRS1860691%�Homo sapiens MCF-7 immortalized cell lineENCBS609QTY at ENCODE: https://www.encodeproject.org/ENCBS609QTY/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7 �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder ČSRA6241702018-05-10 18:11:11
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� �+ �G 3@� ;�eSRR62141982017-10-25�3. ��bL5^�SRX3322945!��ENCODE biosample ENCBS110CZNSRS1860750%�Homo sapiens MCF-7 immortalized cell lineENCBS110CZN at ENCODE: https://www.encodeproject.org/ENCBS110CZN/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdfdev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder čSRA6241712018-05-10 18:11:11
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� �+ �G 3@� ;�dSRR62141972017-10-25ŗ= e�V"5^�SRX3322944!��ENCODE biosample ENCBS764AUTSRS1860751%�Homo sapiens MCF-7 immortalized cell lineENCBS764AUT at ENCODE: https://www.encodeproject.org/ENCBS764AUT/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdfdev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7 �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder čSRA6241712018-05-10 18:11:11
I I �3�OS ! ! ! E! _�' �5 � #�
� �+ �G 3@�;��SRR62143462017-10-25�Q% G�25_ SRX3323023!ӖENCODE biosample ENCBS200IWRSRS1860706%�Homo sapiens MCF-7 immortalized cell lineENCBS200IWR at ENCODE: https://www.encodeproject.org/ENCBS200IWR/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder ��SRA6242242018-05-10 18:11:11
I I �3�PS ! ! ! E! _�' �5 � #�
� �+ �G 3@�;��SRR62143452017-10-25K�� �5_
SRX3323022!һENCODE biosample ENCBS547AXBSRS1860470%�Homo sapiens MCF-7 immortalized cell lineENCBS547AXB at ENCODE: https://www.encodeproject.org/ENCBS547AXB/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7 �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder ��SRA6242242018-05-10 18:11:11
I I �3�QS ! ! ! E! _�' �5 � #�
� �+ �G 3@�;�<SRR62144132017-10-25 l> �oh�5_MSRX3323089!�0ENCODE biosample ENCBS488MMMSRS1860859%�Homo sapiens MCF-7 immortalized cell lineENCBS488MMM at ENCODE: https://www.encodeproject.org/ENCBS488MMM/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7 �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder ��SRA6242692018-05-10 18:11:11
� I � �H�SO ! ! ! ! U �# � �7% 3A�;�QSRR62400662017-10-31'V ���5��SRX3347394,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�3�RS ! ! ! E! _�' �5 � #�
� �+ �G 3@�;�=SRR62144142017-10-25G� ̴zv5_NSRX3323090!�ENCODE biosample ENCBS670IYVSRS1860582%�Homo sapiens MCF-7 immortalized cell lineENCBS670IYV at ENCODE: https://www.encodeproject.org/ENCBS670IYV/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7 �GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, Snyder ��SRA6242692018-05-10 18:11:11
h �h �H�UO ! ! ! ! U �# � �7% 3A�;�7SRR62400402017-10-31"dC
5��5��SRX3347420,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�TO ! ! ! ! U �# � �7% 3A�;�1SRR62400342017-10-31x$��5��SRX3347426,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�WO ! ! ! ! U �# � �7% 3A�;�DSRR62400532017-10-31w���d5��SRX3347407,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�VO ! ! ! ! U �# � �7% 3A�;�+SRR62400282017-10-31 U� �q�5��SRX3347432,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�YO ! ! ! ! U �# � �7% 3A�;�VSRR62400712017-10-31���5��SRX3347389,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�XO ! ! ! ! U �# � �7% 3A�;�BSRR62400512017-10-31 ��x��5��SRX3347409,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�[O ! ! ! ! U �# � �7% 3A�;�"SRR62400192017-10-31 �F�$�5��SRX3347441,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�ZO ! ! ! ! U �# � �7% 3A�;�2SRR62400352017-10-31 �"�5��SRX3347425,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�]O ! ! ! ! U �# � �7% 3A�;�>SRR62400472017-10-31 y.���5��SRX3347413,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�\O ! ! ! ! U �# � �7% 3A�;�=SRR62400462017-10-31� �Q45��SRX3347414,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�_O ! ! ! ! U �# � �7% 3A�;�-SRR62400302017-10-31 E��|5��SRX3347430,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�^O ! ! ! ! U �# � �7% 3A�;�GSRR62400562017-10-31�SAؤ5��SRX3347404,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�aO ! ! ! ! U �# � �7% 3A�;�CSRR62400522017-10-31 �; `M�5��SRX3347408,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�`O ! ! ! ! U �# � �7% 3A�;�ESRR62400542017-10-319�� \�5��SRX3347406,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�cO ! ! ! ! U �# � �7% 3A�;�OSRR62400642017-10-310;Q��5��SRX3347396,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�bO ! ! ! ! U �# � �7% 3A�;�0SRR62400332017-10-31%~4 !wp5��SRX3347427,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�eO ! ! ! ! U �# � �7% 3A�;�4SRR62400372017-10-31 8v D�5��SRX3347423,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�dO ! ! ! ! U �# � �7% 3A�;�XSRR62400732017-10-31# �
l�5��SRX3347387,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�gO ! ! ! ! U �# � �7% 3A�;�,SRR62400292017-10-31"`�
4��5��SRX3347431,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�fO ! ! ! ! U �# � �7% 3A�;�YSRR62400742017-10-31 �5�o�5��SRX3347386,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�iO ! ! ! ! U �# � �7% 3A�;�SSRR62400682017-10-31"��S�5��SRX3347392,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�hO ! ! ! ! U �# � �7% 3A�;�!SRR62400182017-10-31X8�0�5��SRX3347442,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�kO ! ! ! ! U �# � �7% 3A�;�9SRR62400422017-10-31 3r �E�5��SRX3347418,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�jO ! ! ! ! U �# � �7% 3A�;�.SRR62400312017-10-31!�9�5��SRX3347429,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�mO ! ! ! ! U �# � �7% 3A�;�$SRR62400212017-10-31!�� ��x5��SRX3347439,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�lO ! ! ! ! U �# � �7% 3A�;�%SRR62400222017-10-31Ӄz��5��SRX3347438,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�oO ! ! ! ! U �# � �7% 3A�;�JSRR62400592017-10-31��h�<5��SRX3347401,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�nO ! ! ! ! U �# � �7% 3A�;�<SRR62400452017-10-31�
o�5��SRX3347415,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�qO ! ! ! ! U �# � �7% 3A�;�PSRR62400652017-10-31 �4�Cp5��SRX3347395,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�pO ! ! ! ! U �# � �7% 3A�;�KSRR62400602017-10-31&�l ��5��SRX3347400,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�sO ! ! ! ! U �# � �7% 3A�;�ZSRR62400752017-10-31Q�8N45��SRX3347385,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�rO ! ! ! ! U �# � �7% 3A�;�WSRR62400722017-10-31"�B
M��5��SRX3347388,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�uO ! ! ! ! U �# � �7% 3A�;�LSRR62400612017-10-31#D�
x^5��SRX3347399,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�tO ! ! ! ! U �# � �7% 3A�;�/SRR62400322017-10-31#��
�� 5��SRX3347428,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�wO ! ! ! ! U �# � �7% 3A�;�MSRR62400622017-10-31%O� ��5��SRX3347398,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�vO ! ! ! ! U �# � �7% 3A�;�)SRR62400262017-10-31$�
�F�5��SRX3347434,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�yO ! ! ! ! U �# � �7% 3A�;�USRR62400702017-10-31
���5��SRX3347390,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�xO ! ! ! ! U �# � �7% 3A�;�@SRR62400492017-10-31 � ,0�5��SRX3347411,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�{O ! ! ! ! U �# � �7% 3A�;�ISRR62400582017-10-31!�
DL5��SRX3347402,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�zO ! ! ! ! U �# � �7% 3A�;�ASRR62400502017-10-31�C� �5��SRX3347410,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�}O ! ! ! ! U �# � �7% 3A�;� SRR62400142017-10-31��96P5��SRX3347446,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�|O ! ! ! ! U �# � �7% 3A�;�TSRR62400692017-10-31 �}�Q 5��SRX3347391,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3A�;�FSRR62400552017-10-31*7/ �a�5��SRX3347405,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�~O ! ! ! ! U �# � �7% 3A�;�(SRR62400252017-10-31 Z�k�5��SRX3347435,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3A�;�&SRR62400232017-10-31��|�5��SRX3347437,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H� O ! ! ! ! U �# � �7% 3A�;� SRR62400152017-10-31�4*P5��SRX3347445,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3A�;�5SRR62400382017-10-31 fp�i@5��SRX3347422,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3A�;�:SRR62400432017-10-31 '!��5��SRX3347417,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3A�;�RSRR62400672017-10-31dx�Ӡ5��SRX3347393,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3A�;�8SRR62400412017-10-31p/%M�5��SRX3347419,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3A;�*SRR62400272017-10-31�g�5��SRX3347433,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3A ;�HSRR62400572017-10-31��6�5��SRX3347403,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H� O ! ! ! ! U �# � �7% 3A;�SRR62400122017-10-31
�:�85��SRX3347448,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3A;�?SRR62400482017-10-31 >E�||5��SRX3347412,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H� O ! ! ! ! U �# � �7% 3A;�#SRR62400202017-10-31(�T @�5��SRX3347440,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�
O ! ! ! ! U �# � �7% 3A;�'SRR62400242017-10-31o���5��SRX3347436,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�
O ! ! ! ! U �# � �7% 3A;�;SRR62400442017-10-31 ���<5��SRX3347416,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H� O ! ! ! ! U �# � �7% 3A;�3SRR62400362017-10-31�����5��SRX3347424,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3A ;� SRR62400172017-10-31�d�5��SRX3347443,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3A;�6SRR62400392017-10-31%i� b�5��SRX3347421,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3A ;� SRR62400162017-10-319�p�5��SRX3347444,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3A
;� SRR62400132017-10-31��f�5��SRX3347447,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3AH;�SRR62402532017-11-01 }@�/ 5�SRX3347573,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3A ;�NSRR62400632017-10-31+ � �&�5��SRX3347397,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̵SRA6268212018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3AJ;�SRR62402562017-11-01IͰt5� SRX3347570,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3AI;�SRR62402592017-11-01� b�5� SRX3347567,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3AL;�SRR62402232017-11-01 �� �/`5�-SRX3347603,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3AK;�SRR62402642017-11-01 �� 2 �5�SRX3347562,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3AN;�qSRR62402022017-11-01ՋCeD5�BSRX3347624,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3AM;�SRR62402352017-11-010v�cK5�!SRX3347591,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�O ! ! ! ! U �# � �7% 3AP;�SRR62402402017-11-01
C� '�5� SRX3347586,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�O ! ! ! ! U �# � �7% 3AO;�SRR62402582017-11-01B&O�5�
SRX3347568,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H� O ! ! ! ! U �# � �7% 3AR;�SRR62402162017-11-01k�$�5�4SRX3347610,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H� O ! ! ! ! U �# � �7% 3AQ;�SRR62402572017-11-01�,R�5� SRX3347569,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H� O ! ! ! ! U �# � �7% 3AT;�vSRR62402072017-11-019*0�x5�=SRX3347619,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H� O ! ! ! ! U �# � �7% 3AS;�SRR62402432017-11-010�;zA�5�SRX3347583,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�!O ! ! ! ! U �# � �7% 3AV;�SRR62402192017-11-01'�� �W\5�1SRX3347607,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H� O ! ! ! ! U �# � �7% 3AU;�SRR62402442017-11-015��5�SRX3347582,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�#O ! ! ! ! U �# � �7% 3AX;�|SRR62402132017-11-01 �! .e�5�7SRX3347613,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�"O ! ! ! ! U �# � �7% 3AW;�fSRR62401912017-11-01��p5�MSRX3347635,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�%O ! ! ! ! U �# � �7% 3AZ;�SRR62402512017-11-01 ���D5�SRX3347575,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�$O ! ! ! ! U �# � �7% 3AY;�kSRR62401962017-11-01��L 5�HSRX3347630,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�'O ! ! ! ! U �# � �7% 3A\;�SRR62402342017-11-014�r �5�"SRX3347592,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�&O ! ! ! ! U �# � �7% 3A[;�eSRR62401902017-11-01!M` �5�NSRX3347636,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�)O ! ! ! ! U �# � �7% 3A^;�SRR62402392017-11-01,�
KhP5� SRX3347587,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�(O ! ! ! ! U �# � �7% 3A];�SRR62402552017-11-01$ �
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SRX3347571,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�+O ! ! ! ! U �# � �7% 3A`;�dSRR62401892017-11-01�N�'(5�OSRX3347637,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�*O ! ! ! ! U �# � �7% 3A_;�~SRR62402152017-11-01)q� M��5�5SRX3347611,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�-O ! ! ! ! U �# � �7% 3Ab;�SRR62402672017-11-01Ď�Z(5�SRX3347559,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�,O ! ! ! ! U �# � �7% 3Aa;�SRR62402202017-11-01*~0 �v@5�0SRX3347606,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�/O ! ! ! ! U �# � �7% 3Ad;�oSRR62402002017-11-01 "��ch5�DSRX3347626,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�.O ! ! ! ! U �# � �7% 3Ac;�zSRR62402112017-11-01!
P ��5�9SRX3347615,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�1O ! ! ! ! U �# � �7% 3Af;�SRR62402602017-11-01 �[�O5�SRX3347566,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�0O ! ! ! ! U �# � �7% 3Ae;�SRR62402382017-11-01+0 �n@5� SRX3347588,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�3O ! ! ! ! U �# � �7% 3Ah;�SRR62402692017-11-01 �U�)<5��SRX3347557,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�2O ! ! ! ! U �# � �7% 3Ag;�rSRR62402032017-11-01��f,5�ASRX3347623,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�5O ! ! ! ! U �# � �7% 3Aj;�SRR62402252017-11-01,cT
-|�5�+SRX3347601,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�4O ! ! ! ! U �# � �7% 3Ai;�_SRR62401842017-11-01h��!�5�TSRX3347642,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�7O ! ! ! ! U �# � �7% 3Al;�SRR62402332017-11-01r�^ $5�#SRX3347593,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�6O ! ! ! ! U �# � �7% 3Ak;�tSRR62402052017-11-01!;� �(5�?SRX3347621,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�9O ! ! ! ! U �# � �7% 3An;�\SRR62401812017-11-01 ��w D5�WSRX3347645,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�8O ! ! ! ! U �# � �7% 3Am;�SRR62402362017-11-01&�� y+�5� SRX3347590,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�;O ! ! ! ! U �# � �7% 3Ap;�`SRR62401852017-11-01��i�5�SSRX3347641,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�:O ! ! ! ! U �# � �7% 3Ao;�SRR62402172017-11-01)� l(�5�3SRX3347609,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�=O ! ! ! ! U �# � �7% 3Ar;�gSRR62401922017-11-01 ���f�5�LSRX3347634,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�<O ! ! ! ! U �# � �7% 3Aq;�SRR62402702017-11-01%f^ c�5��SRX3347556,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�?O ! ! ! ! U �# � �7% 3At;�SRR62402282017-11-01U��th5�(SRX3347598,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�>O ! ! ! ! U �# � �7% 3As;�^SRR62401832017-11-01-����5�USRX3347643,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�AO ! ! ! ! U �# � �7% 3Av;�mSRR62401982017-11-01�j 'x5�FSRX3347628,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�@O ! ! ! ! U �# � �7% 3Au;�SRR62402662017-11-01��ft5�SRX3347560,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�CO ! ! ! ! U �# � �7% 3Ax;�sSRR62402042017-11-01�I�x5�@SRX3347622,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�BO ! ! ! ! U �# � �7% 3Aw;�SRR62402722017-11-01'� ��5��SRX3347554,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�EO ! ! ! ! U �# � �7% 3Az;�SRR62402422017-11-01 �� �l�5�SRX3347584,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�DO ! ! ! ! U �# � �7% 3Ay;�SRR62402622017-11-01t����5�SRX3347564,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�GO ! ! ! ! U �# � �7% 3A|;�SRR62402302017-11-01D��_�5�&SRX3347596,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�FO ! ! ! ! U �# � �7% 3A{;�SRR62402522017-11-01,=e" 5�SRX3347574,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�IO ! ! ! ! U �# � �7% 3A~;�jSRR62401952017-11-01 ��B�5�ISRX3347631,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�HO ! ! ! ! U �# � �7% 3A};�xSRR62402092017-11-01 )� �l�5�;SRX3347617,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�KO ! ! ! ! U �# � �7% 3A�;�SRR62402732017-11-01 v� WH�5��SRX3347553,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�JO ! ! ! ! U �# � �7% 3A;�nSRR62401992017-11-01�eJ��5�ESRX3347627,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�MO ! ! ! ! U �# � �7% 3A�;�SRR62402212017-11-01 < ;1�5�/SRX3347605,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�LO ! ! ! ! U �# � �7% 3A�;�SRR62402372017-11-012�cd5� SRX3347589,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�OO ! ! ! ! U �# � �7% 3A�;�SRR62402312017-11-011T��5�5�%SRX3347595,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�NO ! ! ! ! U �# � �7% 3A�;�SRR62402182017-11-012�9��5�2SRX3347608,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�QO ! ! ! ! U �# � �7% 3A�;�{SRR62402122017-11-01%
�F5�8SRX3347614,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�PO ! ! ! ! U �# � �7% 3A�;�SRR62402632017-11-01&�� s��5�SRX3347563,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�SO ! ! ! ! U �# � �7% 3A�;�SRR62402472017-11-01:��w�5�SRX3347579,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�RO ! ! ! ! U �# � �7% 3A�;�SRR62402482017-11-01 ��`5�SRX3347578,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�UO ! ! ! ! U �# � �7% 3A�;�iSRR62401942017-11-01&qC i��5�JSRX3347632,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�TO ! ! ! ! U �# � �7% 3A�;�SRR62402612017-11-01�?�5�SRX3347565,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�WO ! ! ! ! U �# � �7% 3A�;�SRR62402652017-11-01t By45�SRX3347561,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�VO ! ! ! ! U �# � �7% 3A�;�SRR62402242017-11-01%�W 0
�5�,SRX3347602,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�YO ! ! ! ! U �# � �7% 3A�;�ySRR62402102017-11-016�p=�@5�:SRX3347616,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�XO ! ! ! ! U �# � �7% 3A�;�SRR62402452017-11-01 �s��$5�SRX3347581,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�[O ! ! ! ! U �# � �7% 3A�;�SRR62402262017-11-01!�
5�*SRX3347600,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�ZO ! ! ! ! U �# � �7% 3A�;�SRR62402272017-11-01���:�5�)SRX3347599,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�]O ! ! ! ! U �# � �7% 3A�;�SRR62402412017-11-01$�y
���5�SRX3347585,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�\O ! ! ! ! U �# � �7% 3A�;�SRR62402492017-11-011�a�p�5�SRX3347577,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�_O ! ! ! ! U �# � �7% 3A�;�bSRR62401872017-11-01'_��45�QSRX3347639,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�^O ! ! ! ! U �# � �7% 3A�;�[SRR62401802017-11-01�'Q�5�XSRX3347646,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�aO ! ! ! ! U �# � �7% 3A�;�SRR62402222017-11-01"]
3��5�.SRX3347604,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�`O ! ! ! ! U �# � �7% 3A�;�SRR62402502017-11-01s�BO�5�SRX3347576,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�cO ! ! ! ! U �# � �7% 3A�;�wSRR62402082017-11-01 ���`5�<SRX3347618,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�bO ! ! ! ! U �# � �7% 3A�;�lSRR62401972017-11-01� Pf�5�GSRX3347629,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�eO ! ! ! ! U �# � �7% 3A�;�SRR62402712017-11-01(�� ��5��SRX3347555,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�dO ! ! ! ! U �# � �7% 3A�;�hSRR62401932017-11-01 ����|5�KSRX3347633,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�gO ! ! ! ! U �# � �7% 3A�;�cSRR62401882017-11-01-�ŏ\5�PSRX3347638,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�fO ! ! ! ! U �# � �7% 3A�;�aSRR62401862017-11-01�t�zp5�RSRX3347640,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�iO ! ! ! ! U �# � �7% 3A�;�SRR62402542017-11-01 P ���5�SRX3347572,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�hO ! ! ! ! U �# � �7% 3A�;�]SRR62401822017-11-01U/9I�5�VSRX3347644,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�kO ! ! ! ! U �# � �7% 3A�;�SRR62402682017-11-01 � J�5� SRX3347558,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�jO ! ! ! ! U �# � �7% 3A�;�uSRR62402062017-11-01?G~�5�>SRX3347620,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�mO ! ! ! ! U �# � �7% 3A�;�SRR62402462017-11-01���`5�SRX3347580,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�lO ! ! ! ! U �# � �7% 3A�;�}SRR62402142017-11-017��� �5�6SRX3347612,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
h �h �H�oO ! ! ! ! U �# � �7% 3A�;�SRR62402322017-11-01&�� �+5�$SRX3347594,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11�H�nO ! ! ! ! U �# � �7% 3A�;�SRR62402292017-11-01` ��5�'SRX3347597,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
� �� �'�qN ! ! ! ! # � �7% 3Ad<<:SRR62698512017-11-09
a�? s�L�5��SRX3375957/�oSRS2646464��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�H�pO ! ! ! ! U �# � �7% 3A�;�pSRR62402012017-11-01 ��}F�5�CSRX3347625,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens ̶SRA6268282018-05-10 18:11:11
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�� �'�sN ! ! ! ! # � �7% 3Ad><;SRR62698522017-11-08BN� K �5��SRX3375956/�rSRS2646201��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'�rN ! ! ! ! # � �7% 3Ad=<PSRR62698732017-11-08�ݝ f�5�rSRX3375935/�rSRS2646201��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
p �p �'�uN ! ! ! ! # � �7% 3Ad@<>SRR62698552017-11-08�� V�ۓ5��SRX3375953/��SRS2645247��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�a�tO ! ! ! ! U �-# � �7% 3Ad?<NSRR62698712017-11-092 D��5�tSRX3375937-��P10SRS2428598%�synchronous ductal carcinoma in situisolate: P10 || age: 48 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: Tissue, Bulk DNA and single cell || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
� �� �'�wN ! ! ! ! # � �7% 3AdB<CSRR62698602017-11-09�~� ��h5�|SRX3375945/�ISRS2646847��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�K�vO ! ! ! ! U �# � �7% 3AdA<TSRR62698772017-11-08E� U��5�nSRX3375931,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
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�� �K�yO ! ! ! ! U �# � �7% 3AdD<ISRR62698662017-11-09ݠ� �%��5�ySRX3375942,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'�xN ! ! ! ! # � �7% 3AdC<FSRR62698632017-11-08�Ba ����5�~SRX3375947/1�SRS2490581��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
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�p �a�{O ! ! ! ! U �-# � �7% 3AdF<BSRR62698592017-11-09�� !�@5��SRX3375950-��P10SRS2428598%�synchronous ductal carcinoma in situisolate: P10 || age: 48 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: Tissue, Bulk DNA and single cell || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'�zN ! ! ! ! # � �7% 3AdE<RSRR62698752017-11-08#,9 sz��5�pSRX3375933/1�SRS2490581��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
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K�, }��P5�}SRX3375946,�P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'�|N ! ! ! ! # � �7% 3AdG<USRR62698782017-11-09:�J �e25�mSRX3375930/��SRS2645247��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
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�� �K�O ! ! ! ! U �# � �7% 3AdJ<?SRR62698562017-11-08��) ���5��SRX3375952,�wP5SRS2493573%�synchronous ductal carcinoma in situisolate: P5 || age: 47 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'�~N ! ! ! ! # � �7% 3AdI<QSRR62698742017-11-08��� ��5�qSRX3375934/�oSRS2646464��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
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�� �'�N ! ! ! ! # � �7% 3AdL<OSRR62698722017-11-09 �E R�)85�sSRX3375936/�ISRS2646847��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'� N ! ! ! ! # � �7% 3AdK<LSRR62698692017-11-09 3� +��x5�vSRX3375939/�ISRS2646847��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
� �� �'�N ! ! ! ! # � �7% 3AdN<KSRR62698682017-11-08�� �[�@5�wSRX3375940/��SRS2641973��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�K�O ! ! ! ! U �# � �7% 3AdM<JSRR62698672017-11-08( -�_A5�xSRX3375941,�wP5SRS2493573%�synchronous ductal carcinoma in situisolate: P5 || age: 47 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
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-�|p5�{SRX3375944-�BP1SRS2535762%�isolate: P1 || age: 57 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIB || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'�N ! ! ! ! # � �7% 3AdO<HSRR62698652017-11-08�%� ��5�zSRX3375943/��SRS2645247��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
L �L �K�O ! ! ! ! U �# � �7% 3AdR<WSRR62698802017-11-08f +OΩ5�kSRX3375928,�wP5SRS2493573%�synchronous ductal carcinoma in situisolate: P5 || age: 47 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�a�O ! ! ! ! U �-# � �7% 3AdQ<MSRR62698702017-11-08��� ��@5�uSRX3375938-��P10SRS2428598%�synchronous ductal carcinoma in situisolate: P10 || age: 48 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: Tissue, Bulk DNA and single cell || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
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N ! ! ! ! # � �7% 3AdU<DSRR62698612017-11-08:&� Mnf�5��SRX3375949/�oSRS2646464��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'� N ! ! ! ! # � �7% 3AdT<=SRR62698542017-11-09��� Q2oh5��SRX3375954/1�SRS2490581��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'�N ! ! ! ! # � �7% 3AdS<VSRR62698792017-11-08J�e �F5�lSRX3375929/��SRS2641973��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
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� O ! ! ! ! �I# � �7% 3AdW<SSRR62698762017-11-08�G N7x5�oSRX3375932-�BP1SRS2535762%�isolate: P1 || age: 57 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIB || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�'� N ! ! ! ! # � �7% 3AdV<ESRR62698622017-11-08�f ��k5�SRX3375948/�rSRS2646201��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
� ��� � �x�N ! ! ! '! �# '�%% 3A��<��SRR63120572017-11-22��;6Z*SRX3412311(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�z�N ! ! ! '! �# '�%% 3A��<��SRR63120602017-11-22� �u�6Z'SRX3412308(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�'�N ! ! ! ! # � �7% 3AdY<ASRR62698582017-11-09�r� 5Gs5��SRX3375951/��SRS2641973��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11�
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O ! ! ! ! �I# � �7% 3AdX<<SRR62698532017-11-08��| X ��5��SRX3375955-�BP1SRS2535762%�isolate: P1 || age: 57 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIB || BioSampleModel: Human��PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiens �SRA6295742018-05-10 18:11:11
�y�N ! ! ! '! �# '�%% 3A��<��SRR63120542017-11-22 ��t^;6Z-SRX3412314(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�z�N ! ! ! '! �# '�%% 3A��<��SRR63120552017-11-22 �� ���6Z,SRX3412313(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�x�N ! ! ! '! �# '�%% 3A��<��SRR63120492017-11-22P%9Q6Z2SRX3412319(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�y�N ! ! ! '! �# '�%% 3A��<��SRR63120502017-11-22 ��V@�6Z1SRX3412318(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�y�N ! ! ! '! �# '�%% 3A��<��SRR63120532017-11-22 �S]��6Z.SRX3412315(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�y�N ! ! ! '! �# '�%% 3A��<��SRR63120482017-11-22 ��jM�6Z3SRX3412320(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�z�N ! ! ! '! �# '�%% 3A��<��SRR63120522017-11-22��2�6Z/SRX3412316(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�x�N ! ! ! '! �# '�%% 3A��<��SRR63120562017-11-22y�Sks6Z+SRX3412312(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11
� � � N ! ! ! ! # �-�;E 3A�o<�ZSRR63139292017-11-22�9� I 6]�SRX34138550P�SRS2707038jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11� � N ! ! ! ! # �-�;E 3A�n=�SRR63139222017-11-24�;I � _6�0SRX34138620P�SRS2707044jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11�x� N ! ! ! '! �# '�%% 3A�<��SRR63120472017-11-22C )kY6Z4SRX3412321(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�z�N ! ! ! '! �# '�%% 3A�<��SRR63120592017-11-22 � ���6Z(SRX3412309(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�z�N ! ! ! '! �# '�%% 3A�<��SRR63120512017-11-22+� ƞf6Z0SRX3412317(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11�x�N ! ! ! '! �# '�%% 3A� <��SRR63120582017-11-22l Q 6Z)SRX3412310(��Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human��PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiens �SRA6326512018-05-10 18:11:11
� |�t� � �"N ! ! ! ! # �-�;E 3A�s=�SRR63139262017-11-24z7l �`&�6�/SRX34138580P�SRS2707041jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11� �!N ! ! ! ! # �-�;E 3A�r<�XSRR63139252017-11-22r n և�p6]�SRX34138590P�SRS2707058jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11� � N ! ! ! ! # �-�;E 3A�q=�SRR63139212017-11-24p#j �1*g6�1SRX34138630P�SRS2707045jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11� � N ! ! ! ! # �-�;E 3A�p<�YSRR63139272017-11-22�E� ���6]�SRX34138570P�SRS2707040jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11
r |�tH� r �g�(M ! ! ! ! �g 3E�eB�SRR67495852018-02-20 ��3"h�;�^SRX3722244 cT47DSRS1359716%�isolate: T47D breast cancer cells || age: NA || biomaterial_provider: Myles Brown || sex: not determined || tissue: breast cancer || cell_line: T47D || BioSampleModel: Human�SRP133088 �SRA6603742018-05-10 18:11:11�g�'M ! ! ! ! �g 3E�dB�SRR67495832018-02-20�.m.5��;�`SRX3722246 cT47DSRS1359716%�isolate: T47D breast cancer cells || age: NA || biomaterial_provider: Myles Brown || sex: not determined || tissue: breast cancer || cell_line: T47D || BioSampleModel: Human�SRP133088 �SRA6603742018-05-10 18:11:11�(�&M ! ! ! �a 3E=*BY�SRR67090412018-02-12�;.7SRX3683141 �;DRS035236DRS035236%�humandescription: Sample ID: CAGE_6_H12, Run: 1772-123-074, Well: H12, Cell curation: Red, Timepoint: t00, QC pass: TRUE, Lane7 || bioproject_id: PRJDB5282 || dev_stage: 58 years old || cell_line: A549 || cell_type: epithelial || sample_name: CAGE_6_H12 || disease: carcinoma || sex: male || sample_title: CAGE_6_H12 || tissue_type: lung || biomaterial_provider: ATCC �SRP132698 i�SRA6587132018-05-10 18:11:11� �%N ! ! ! ! # �-�;E 3A�v=�SRR63139282017-11-24�$" q�r6�.SRX34138560P�SRS2707039jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11� �$N ! ! ! ! # �-�;E 3A�u<�VSRR63139232017-11-22� ��/6]�SRX34138610P�SRS2707043jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11� �#N ! ! ! ! # �-�;E 3A�t<�WSRR63139242017-11-22j�P ��?6]�SRX34138600P�SRS2707042jPRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6N �SRA6329562018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�4M ! ! ! ! �% 3F �C�aSRR67819042018-02-26�5� 4Ѹ�<G�SRX3741835&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�3M ! ! ! ! �% 3F �C�1SRR67818562018-02-26 #� �1/�<G�SRX3741883&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�2M ! ! ! ! �% 3F �C�dSRR67819072018-02-26f �ɖ�<G�SRX3741832&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�1M ! ! ! ! �% 3F �C�=SRR67818682018-02-26!�B ˟�h<G�SRX3741871&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�0M ! ! ! ! �% 3F �C��SRR67819452018-02-26 �� �dS�<G�SRX3741794&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�/M ! ! ! ! �% 3F �C��SRR67819392018-02-266^ �:*H<G�SRX3741800&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�3�.L ! ! ! ! 3E�kB�SRR67495822018-02-21�^Z.�6�;�aSRX37222475�SRS2979831�SRP133088 �SRA6603742018-05-10 18:11:11�3�-L ! ! ! ! 3E�jB�SRR67495812018-02-21�-.B�;�bSRX37222485�SRS2979831�SRP133088 �SRA6603742018-05-10 18:11:11�g�,M ! ! ! ! �g 3E�iB� SRR67495792018-02-20"g�5\�;�dSRX3722250 cT47DSRS1359716%�isolate: T47D breast cancer cells || age: NA || biomaterial_provider: Myles Brown || sex: not determined || tissue: breast cancer || cell_line: T47D || BioSampleModel: Human�SRP133088 �SRA6603742018-05-10 18:11:11�g�+M ! ! ! ! �g 3E�hB�SRR67495802018-02-20UQ�:T�;�cSRX3722249 cT47DSRS1359716%�isolate: T47D breast cancer cells || age: NA || biomaterial_provider: Myles Brown || sex: not determined || tissue: breast cancer || cell_line: T47D || BioSampleModel: Human�SRP133088 �SRA6603742018-05-10 18:11:11�3�*L ! ! ! ! 3E�gB�SRR67495862018-02-21��&H]�;�]SRX37222435�SRS2979831�SRP133088 �SRA6603742018-05-10 18:11:11�3�)L ! ! ! ! 3E�fB�SRR67495842018-02-21 }�4�H�;�_SRX37222455�SRS2979831�SRP133088 �SRA6603742018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�@M ! ! ! ! �% 3F �C��SRR67819462018-02-26Y � �O|<G�SRX3741793&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�?M ! ! ! ! �% 3F �C��SRR67819412018-02-26�y1 +)6t<G�SRX3741798&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�>M ! ! ! ! �% 3F �C�2SRR67818572018-02-26�w� و" <G�SRX3741882&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�=M ! ! ! ! �% 3F �C�gSRR67819102018-02-266/
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�<M ! ! ! ! �% 3F �C�lSRR67819152018-02-26C`� �`,D<G�SRX3741824&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�;M ! ! ! ! �% 3F �C�QSRR67818882018-02-26\�L �"�p<G�SRX3741851&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�:M ! ! ! ! �% 3F �C�SRR67819342018-02-26K�� �H��<G�SRX3741805&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�9M ! ! ! ! �% 3F �C�`SRR67819032018-02-26Q�" ���<G�SRX3741836&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�8M ! ! ! ! �% 3F �C�^SRR67819012018-02-26~j+ �<<G�SRX3741838&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�7M ! ! ! ! �% 3F �C�_SRR67819022018-02-269 � � H�<G�SRX3741837&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�6M ! ! ! ! �% 3F �C�5SRR67818602018-02-262� �ˡ`<G�SRX3741879&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�LM ! ! ! ! �% 3F �C�ISRR67818802018-02-26��g L�l<G�SRX3741859&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�KM ! ! ! ! �% 3F �C�GSRR67818782018-02-26�� y�W�<G�SRX3741861&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�JM ! ! ! ! �% 3F �C�ySRR67819282018-02-26��� �a�0<G�SRX3741811&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�IM ! ! ! ! �% 3F �C�;SRR67818662018-02-26�8� �<<G�SRX3741873&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�HM ! ! ! ! �% 3F �C�,SRR67818512018-02-260
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�GM ! ! ! ! �% 3F �C�ZSRR67818972018-02-26 W� � Ј<G�SRX3741842&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�FM ! ! ! ! �% 3F �C�)SRR67818482018-02-26f�� �f� <G�SRX3741891&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�EM ! ! ! ! �% 3F �C�ESRR67818762018-02-26Y�� �G��<G�SRX3741863&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�DM ! ! ! ! �% 3F �C�@SRR67818712018-02-26� � lH<G�SRX3741868&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�CM ! ! ! ! �% 3F �C�JSRR67818812018-02-26�L up<G�SRX3741858&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�BM ! ! ! ! �% 3F �C�kSRR67819142018-02-26C�� �8<G�SRX3741825&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�XM ! ! ! ! �% 3F �C�/SRR67818542018-02-26[tT �M�<G�SRX3741885&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�WM ! ! ! ! �% 3F �C�{SRR67819302018-02-26KR� �H<G�SRX3741809&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�VM ! ! ! ! �% 3F �C�qSRR67819202018-02-26��� H�<G�SRX3741819&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�UM ! ! ! ! �% 3F �C�}SRR67819322018-02-26=�� �bg�<G�SRX3741807&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�TM ! ! ! ! �% 3F �C�RSRR67818892018-02-26]oY ��J�<G�SRX3741850&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�SM ! ! ! ! �% 3F �C�KSRR67818822018-02-26�Rz ����<G�SRX3741857&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�RM ! ! ! ! �% 3F �C�bSRR67819052018-02-26)u �&VH<G�SRX3741834&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�QM ! ! ! ! �% 3F �C��SRR67819382018-02-26�� (
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�PM ! ! ! ! �% 3F �C�eSRR67819082018-02-26 �Bq �ηt<G�SRX3741831&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�OM ! ! ! ! �% 3F �C�8SRR67818632018-02-26Uis �$�<G�SRX3741876&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�NM ! ! ! ! �% 3F �C�cSRR67819062018-02-26i�G �_i�<G�SRX3741833&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�dM ! ! ! ! �% 3F �C�7SRR67818622018-02-26 �QY �a2�<G�SRX3741877&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�cM ! ! ! ! �% 3F �C��SRR67819352018-02-26?�! ��4<G�SRX3741804&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�bM ! ! ! ! �% 3F �C�WSRR67818942018-02-26q�^ ��<G�SRX3741845&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�aM ! ! ! ! �% 3F �C�USRR67818922018-02-26 �� ��!<<G�SRX3741847&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�`M ! ! ! ! �% 3F �C�?SRR67818702018-02-26�� �J�<G�SRX3741869&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�_M ! ! ! ! �% 3F �C��SRR67819362018-02-26N�� �gL$<G�SRX3741803&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�^M ! ! ! ! �% 3F �C�OSRR67818862018-02-26�uZ ,��H<G�SRX3741853&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�]M ! ! ! ! �% 3F �C�LSRR67818832018-02-26�� Tް<G�SRX3741856&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�\M ! ! ! ! �% 3F �C�HSRR67818792018-02-26 � q�J�<G�SRX3741860&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�[M ! ! ! ! �% 3F �C�PSRR67818872018-02-26�4� )��\<G�SRX3741852&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�I�ZM ! ! ! ! �% 3F �C��SRR67819442018-02-26y{:Uj��<G�SRX3741795&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�J�pM ! ! ! ! �% 3F �C�fSRR67819092018-02-26 �Y�]��T<G�SRX3741830&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�oM ! ! ! ! �% 3F �C�:SRR67818652018-02-26U� ��@<G�SRX3741874&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�nM ! ! ! ! �% 3F �C�<SRR67818672018-02-26�O� /D�<G�SRX3741872&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�mM ! ! ! ! �% 3F �C�MSRR67818842018-02-26�� �%� <G�SRX3741855&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�lM ! ! ! ! �% 3F �C�*SRR67818492018-02-26�- � �<G�SRX3741890&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�kM ! ! ! ! �% 3F �C�jSRR67819132018-02-26=a� �(��<G�SRX3741826&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�jM ! ! ! ! �% 3F �C�BSRR67818732018-02-26��
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�iM ! ! ! ! �% 3F �C�ASRR67818722018-02-26>Q� ��d�<G�SRX3741867&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�hM ! ! ! ! �% 3F �C�-SRR67818522018-02-26 E� p�,�<G�SRX3741887&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�gM ! ! ! ! �% 3F �C�DSRR67818752018-02-26�� �r,<G�SRX3741864&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�fM ! ! ! ! �% 3F �C��SRR67819372018-02-26 ߳ �MI�<G�SRX3741802&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�|M ! ! ! ! �% 3F C�CSRR67818742018-02-261C� ֣��<G�SRX3741865&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�{M ! ! ! ! �% 3F C�pSRR67819192018-02-26;D� ݬ|D<G�SRX3741820&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�zM ! ! ! ! �% 3F C��SRR67819422018-02-26uST ~�<G�SRX3741797&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�yM ! ! ! ! �% 3F C�VSRR67818932018-02-26Pv �E�<G�SRX3741846&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�xM ! ! ! ! �% 3F C��SRR67819402018-02-268?i ی��<G�SRX3741799&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�J�wM ! ! ! ! �% 3F C��SRR67819432018-02-26 ��nO��<G�SRX3741796&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�vM ! ! ! ! �% 3F C�>SRR67818692018-02-26[� � , <G�SRX3741870&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�uM ! ! ! ! �% 3F �C�\SRR67818992018-02-26��r ��(<G�SRX3741840&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�tM ! ! ! ! �% 3F �C�9SRR67818642018-02-26 A ���<G�SRX3741875&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�sM ! ! ! ! �% 3F �C�SSRR67818902018-02-26z �&��<G�SRX3741849&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�rM ! ! ! ! �% 3F �C�XSRR67818952018-02-26R�� ���<G�SRX3741844&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�|SRR67819312018-02-26� Ŗ�<G�SRX3741808&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�FSRR67818772018-02-26�ho �n <G�SRX3741862&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�oSRR67819182018-02-26ğ� >@_�<G�SRX3741821&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�wSRR67819262018-02-26��� D�H<G�SRX3741813&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C��SRR67819472018-02-26O�E T $�<G�SRX3741792&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�YSRR67818962018-02-26e�� ��[�<G�SRX3741843&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�[SRR67818982018-02-26Bp@ �� <G�SRX3741841&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L� M ! ! ! ! �% 3F
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�vSRR67819252018-02-26UU� � %<G�SRX3741814&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�~M ! ! ! ! �% 3F C�zSRR67819292018-02-26�2 *��(<G�SRX3741810&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�M ! ! ! ! �% 3F*dDZ�SRR67996982018-03-03Z,�Fs �<�1SRX3758472&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�M ! ! ! ! �% 3F*cDZ�SRR67997252018-03-03#�d <�SRX3758445&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�~SRR67819332018-02-26_( ��!h<G�SRX3741806&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�6SRR67818612018-02-26�d� +�� <G�SRX3741878&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�nSRR67819172018-02-268� �c��<G�SRX3741822&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�rSRR67819212018-02-26HnE �툄<G�SRX3741818&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�M ! ! ! ! �% 3F C�hSRR67819112018-02-26ܓ� O�8<G�SRX3741828&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L� M ! ! ! ! �% 3F C�sSRR67819222018-02-26%�� �{| <G�SRX3741817&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L� M ! ! ! ! �% 3F C�iSRR67819122018-02-26!�z ����<G�SRX3741827&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11�L�
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 ��SRA6621022018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I� M ! ! ! ! �% 3F*pDZ�SRR67996892018-03-03$�p �G�<�:SRX3758481&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I� M ! ! ! ! �% 3F*oDZ�SRR67996772018-03-03��gg�<�FSRX3758493&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I� M ! ! ! ! �% 3F*nDZ�SRR67996952018-03-03C!�4r[�<�4SRX3758475&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I� M ! ! ! ! �% 3F*mD[SRR67997602018-03-05.�\.�$\<��SRX3758410&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I� M ! ! ! ! �% 3F*lDZ�SRR67997032018-03-03@��2�,<�,SRX3758467&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�M ! ! ! ! �% 3F*kDZ�SRR67996922018-03-03-�#�5<�7SRX3758478&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�M ! ! ! ! �% 3F*jDZ�SRR67997342018-03-03jg ��l<�
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�M ! ! ! ! �% 3F*iD[SRR67997582018-03-030>e%���<�SRX3758412&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�M ! ! ! ! �% 3F*hDZ�SRR67996872018-03-03@_�2J�`<�<SRX3758483&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�M ! ! ! ! �% 3F*gDZ�SRR67997182018-03-03LF�;�B<� SRX3758452&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�M ! ! ! ! �% 3F*fDZ�SRR67997452018-03-05p�$rK h<�SRX3758425&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�,M ! ! ! ! �% 3F*|DZ�SRR67996822018-03-03 �P�f�<�ASRX3758488&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�+M ! ! ! ! �% 3F*{DZ�SRR67997442018-03-05-(�-}G<�SRX3758426&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�*M ! ! ! ! �% 3F*zDZ�SRR67997312018-03-03xհ $�?�<�SRX3758439&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�)M ! ! ! ! �% 3F*yDZ�SRR67996852018-03-030��<�>SRX3758485&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�(M ! ! ! ! �% 3F*xDZ�SRR67997412018-03-036�C*��X<�SRX3758429&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�'M ! ! ! ! �% 3F*wDZ�SRR67997282018-03-03��] ����<�SRX3758442&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�&M ! ! ! ! �% 3F*vDZ�SRR67997502018-03-03 �^N�p<�SRX3758420&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�%M ! ! ! ! �% 3F*uDZ�SRR67997422018-03-03D�s5�9�<�SRX3758428&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�$M ! ! ! ! �% 3F*tDZ�SRR67997382018-03-03F.66�0<� SRX3758432&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�#M ! ! ! ! �% 3F*sDZ�SRR67997052018-03-03sb "$� <�*SRX3758465&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�"M ! ! ! ! �% 3F*rDZ�SRR67997512018-03-03-8�#TD<�SRX3758419&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�8M ! ! ! ! �% 3F*�DZ�SRR67997192018-03-03VKCD��<� SRX3758451&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�7M ! ! ! ! �% 3F*�DZ�SRR67997202018-03-03j�`S�� <�SRX3758450&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�6M ! ! ! ! �% 3F*�DZ�SRR67997472018-03-05`��_��<� SRX3758423&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�5M ! ! ! ! �% 3F*�DZ�SRR67997292018-03-03.�a$���<�SRX3758441&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�4M ! ! ! ! �% 3F*�DZ�SRR67997082018-03-06�� ��6�<�'SRX3758462&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�3M ! ! ! ! �% 3F*�DZ�SRR67996862018-03-03 � b<�=SRX3758484&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�2M ! ! ! ! �% 3F*�DZ�SRR67996992018-03-03"��?��<�0SRX3758471&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�1M ! ! ! ! �% 3F*�DZ�SRR67997272018-03-032��'���<�SRX3758443&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�0M ! ! ! ! �% 3F*�DZ�SRR67997012018-03-03=0 9�<�.SRX3758469&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�/M ! ! ! ! �% 3F*DZ�SRR67996762018-03-03"��;�<�GSRX3758494&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�.M ! ! ! ! �% 3F*~DZ�SRR67997072018-03-03~�- + �(<�(SRX3758463&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�CM ! ! ! ! �% 3F*�DZ�SRR67996882018-03-03C�5��<�;SRX3758482&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�BM ! ! ! ! �% 3F*�DZ�SRR67997482018-03-036� *��<�SRX3758422&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�AM ! ! ! ! �% 3F*�DZ�SRR67997212018-03-03F�\7??�<�SRX3758449&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�@M ! ! ! ! �% 3F*�DZ�SRR67996792018-03-03-��#�(<�DSRX3758491&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�?M ! ! ! ! �% 3F*�DZ�SRR67997492018-03-03Cx
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�>M ! ! ! ! �% 3F*�DZ�SRR67997132018-03-03o� �&�<�"SRX3758457&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�=M ! ! ! ! �% 3F*�DZ�SRR67997142018-03-03��� A���<�!SRX3758456&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�<M ! ! ! ! �% 3F*�DZ�SRR67996912018-03-03 '
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�;M ! ! ! ! �% 3F*�D[SRR67997572018-03-03<u.��h<�SRX3758413&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�:M ! ! ! ! �% 3F*�DZ�SRR67997372018-03-03 �)��<�
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�OM ! ! ! ! �% 3F*�DZ�SRR67997302018-03-038�M,W(<�SRX3758440&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�NM ! ! ! ! �% 3F*�DZ�SRR67997112018-03-03"8� �l�<�$SRX3758459&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�MM ! ! ! ! �% 3F*�DZ�SRR67996932018-03-03,\"��h<�6SRX3758477&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�LM ! ! ! ! �% 3F*�DZ�SRR67997042018-03-03?;�1f�<�+SRX3758466&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�KM ! ! ! ! �% 3F*�DZ�SRR67997322018-03-03t� "=�,<�SRX3758438&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�JM ! ! ! ! �% 3F*�D[SRR67997612018-03-05>��=��<��SRX3758409&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�IM ! ! ! ! �% 3F*�DZ�SRR67997232018-03-03 {5`Ah<�SRX3758447&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�HM ! ! ! ! �% 3F*�DZ�SRR67996782018-03-03-[J#oQ�<�ESRX3758492&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�GM ! ! ! ! �% 3F*�DZ�SRR67996842018-03-03+.!�s�<�?SRX3758486&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�FM ! ! ! ! �% 3F*�DZ�SRR67997172018-03-03N��=�@(<� SRX3758453&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�[M ! ! ! ! �% 3F*�DZ�SRR67997152018-03-03%K4 "��<� SRX3758455&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�ZM ! ! ! ! �% 3F*�D[SRR67997562018-03-030ͻ& �<�SRX3758414&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�YM ! ! ! ! �% 3F*�DZ�SRR67997532018-03-05</�;��@<�SRX3758417&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�XM ! ! ! ! �% 3F*�DZ�SRR67996972018-03-0324�'9Mp<�2SRX3758473&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�WM ! ! ! ! �% 3F*�DZ�SRR67997262018-03-03)� Q<�SRX3758444&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�VM ! ! ! ! �% 3F*�DZ�SRR67997242018-03-03*f�! r�<�SRX3758446&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�UM ! ! ! ! �% 3F*�DZ�SRR67997162018-03-03���0<� SRX3758454&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�TM ! ! ! ! �% 3F*�DZ�SRR67996962018-03-03)�� �� <�3SRX3758474&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�SM ! ! ! ! �% 3F*�DZ�SRR67996902018-03-03 �M��(<�9SRX3758480&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�RM ! ! ! ! �% 3F*�DZ�SRR67997022018-03-03C�N4���<�-SRX3758468&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11
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BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�gM ! ! ! ! �% 3F*�DZ�SRR67997102018-03-06Ư' �8�x<�%SRX3758460&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�fM ! ! ! ! �% 3F*�DZ�SRR67997432018-03-03 7�+n�<�SRX3758427&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�eM ! ! ! ! �% 3F*�DZ�SRR67996812018-03-03g��x<�BSRX3758489&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�dM ! ! ! ! �% 3F*�DZ�SRR67997542018-03-05`�R`�[(<�SRX3758416&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�cM ! ! ! ! �% 3F*�DZ�SRR67996832018-03-03%�F ^��<�@SRX3758487&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�L�bM ! ! ! ! �% 3F*�DZ�SRR67997092018-03-03m # (X<�&SRX3758461&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�aM ! ! ! ! �% 3F*�DZ�SRR67997392018-03-031��&�h`<�SRX3758431&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�`M ! ! ! ! �% 3F*�D[SRR67997592018-03-03.�u$XCh<��SRX3758411&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�_M ! ! ! ! �% 3F*�DZ�SRR67997462018-03-03&� �\�<�SRX3758424&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11�I�^M ! ! ! ! �% 3F*�D[ SRR67997552018-03-03@�2�[8<�SRX3758415&�
BCSC-LCMSRS2123144%�isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human�SRP103895 �^SRA6639242018-05-10 18:11:11
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��V> �SRX38681376PtSRS3042210v�145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:female �`SRA6777922018-05-10 18:11:11�u�jN ! ! ! ! �;�I 3FѾG0�SRR69207462018-03-30�� ď�> �SRX38681356PvSRS3042212v�145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:female �`SRA6777922018-05-10 18:11:11
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FIʐ> �SRX38681366PySRS3042215v�145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:female �`SRA6777922018-05-10 18:11:11�u�lN ! ! ! ! �;�I 3F�G0�SRR69207392018-03-30ezh �f�> �SRX38681426PsSRS3042208v�145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:female �`SRA6777922018-05-10 18:11:11
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� T�S � ��$O !! Y )I �O 3 W ) ) a9�)/�) E 3@�� DRR006301DRR0063012012-03-212015-10-21Ajv�@ A�TI NIVTSDRX005525@�� DRX005525DRX005525Transcriptional sequence of 'Aka' rootDRP002494DRS005664Aka_rootRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�: DRS005664DRS005664 �#bunching onionRoots of 'Aka'@� DRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onion@�� DRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11�"�#O !! a )I �O 3 W ) = a9�)/�) E 3@�� DRR006306DRR0063062012-03-212015-10-21Ah�n@ A�q%� NIVTSDRX005530@�� DRX005530DRX005530Transcriptional sequence of 'F' pseudostemDRP002494DRS005669Shi_stemRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�? DRS005669DRS005669 �#bunching onionMature pseudostem of 'F'@� DRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onion@�� DRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11�W�"P !! _ )I �M3 W ) �7 a9�)/�) E 3@�� DRR006298DRR0062982012-02-262015-02-04A4�q A��c� NIASDRX005522@�� DRX005522DRX005522Transcriptional sequence of 'Ki' from 454DRP002494DRS005661LIY01RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 450; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 1LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX Titanium@�7 DRS005661DRS005661 �#bunching onionMixture of nine tissues from inbred 'Ki' (2-weeks seedlings, leaf, roots, basal meristem, immature flower bract, mature bract (about 1 week before anthesis), opened flowers, immature fruits and sliced pseudostem).@� DRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onion@�� DRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11�(�!O !! c %)I �O 3 W ) ? a9�)/�) E 3@�� DRR006302DRR0063022012-03-212015-10-21Ai�� Aᤐ� NIVTSDRX005526@�� DRX005526DRX005526Transcriptional sequence of 'Aka' seedlingsDRP002494DRS005665Aka_seedlingRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 180; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�; DRS005665DRS005665 �#bunching onion2-week seedlings of 'Aka'@� DRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onion@�� DRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11
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@ DRS021959DRS021959sex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�%��xQ ! E =) �)# G � u�A� �9 3@�À DRR024746DRR0247462015-12-29A
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@ DRS021959DRS021959sex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�#�%O !! a )I �O 3 W ) A a9�)/�) E 3@�� DRR006305DRR0063052012-03-212015-10-21Aju� A⚶�� NIVTSDRX005529@�� DRX005529DRX005529Transcriptional sequence of 'Ki' meristemsDRP002494DRS005668Ki_meriRNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 190; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 91ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�> DRS005668DRS005668 �#bunching onionMature pseudostem of 'Aka'@� DRP002494DRP002494Allium fistulosum transcriptome sequencingTranscriptome AnalysisTranscriptome sequencing to produce an EST-based genetic map of bunching onionAllium fistulosumTranscriptome sequencing to produce an EST-based genetic map of bunching onion@�� DRA000945NIVTSBreeding and Genome Division2018-05-10 18:11:11
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@ DRS021959DRS021959sex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�3��{Q ! U 3) �)3 W � u�A� �9 3@�� DRR024743DRR0247432015-12-29A!�� A�Rر DRX022407@�?@ DRX022407DRX022407454 GS FLX Titanium sequencing of HBDRP002820DRS021957454-T_Head-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX Titanium@� � DRS021957DRS021957sex: asexual || strain: GI || sample_title: Dj_GI_HB || tissue_type: Head blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�#��zQ ! E ;) �)# G � u�A� �9 3@�� DRR024740DRR0247402015-12-29A5�� A�n@ŀ DRX022404@�>� DRX022404DRX022404454 GS FLX+ sequencing of ABDRP002820DRS021958454-P_Anterior-blastemaRNA-SeqTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1LS454454 GS FLX+INSTRUMENT_MODEL: 454 GS FLX+@�
DRS021958DRS021958sex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11
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DRS021958DRS021958sex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11
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DRS021958DRS021958sex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11�%��Q ! a =)I �Q ) M � u�A� �9 3@�@ DRR024737DRR0247372015-12-29Ah��� A�m4� DRX022401@�=� DRX022401DRX022401Illumina MiSeq paired end sequencing of PBDRP002820DRS021959MiSeq_Posterior-blastemaRNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 316; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 126ILLUMINAIllumina MiSeqINSTRUMENT_MODEL: Illumina MiSeq@�
@ DRS021959DRS021959sex: asexual || strain: GI || sample_title: Dj_GI_PB || tissue_type: Posterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11
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DRS021958DRS021958sex: asexual || strain: GI || sample_title: Dj_GI_AB || tissue_type: Anterior blastema || description: The clonal GI strain reproduced asexually by transverse fission from one animal. || collection_date: 1990 || sample_name: GI || geo_loc_name: Japan:Gifu, Gujo, Iruma River || bioproject_id: PRJDB3117 || env_biome: Small river@�� DRP002820DRP002820Transcriptome sequence of planarian Dugesia japonicaOtherTranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.Dugesia japonica strain:GITranscriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.@�� DRA002722KYOTO_SCLaboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University2018-05-10 18:11:11
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%J �V��bP ! )I �Q 3 W �+ ]�W �W O 3@�� DRR029448DRR0294482015-04-01Ap +� A�Q�� DRX026508@�@� DRX026508DRX026508Illumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�c� DRS019417DRS019417�sex: mix || strain: Ka4C1 || sample_title: B. xylophilus mixed-stage || description: B.xylophilus mixed-stage on B. cinerea || sample_name: BxMixed || bioproject_id: PRJDB3458 || dev_stage: mixed propagative@�� DRP002612DRP002612Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.@�� DRA002992MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11�V��aP ! )I �Q 3 W �+ ]�W �W O 3@�� DRR029449DRR0294492015-04-01Af3f� Aᄏ,� DRX026509@�@� DRX026509DRX026509Illumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�c� DRS019417DRS019417�sex: mix || strain: Ka4C1 || sample_title: B. xylophilus mixed-stage || description: B.xylophilus mixed-stage on B. cinerea || sample_name: BxMixed || bioproject_id: PRJDB3458 || dev_stage: mixed propagative@�� DRP002612DRP002612Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.@�� DRA002992MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11
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Q� AߠI DRX026516@�B� DRX026516DRX026516Illumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002610DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�d� DRS019416DRS019416�sex: mix || strain: Ka4C1 || sample_title: B.xylophilus cont Aug || description: B.xylophilus control in August || sample_name: BxContAug || bioproject_id: PRJDB3458 || dev_stage: mixed propagative@�� DRP002610DRP002610Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.@�� DRA002996MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11�V��cP ! )I �Q 3 W �+ ]�W �W O 3@�� DRR029447DRR0294472015-04-01Ac�x A�!�� DRX026507@�@@ DRX026507DRX026507Illumina HiSeq 2000 paired end sequencing of SAMD00025070DRP002612DRS019417RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�c� DRS019417DRS019417�sex: mix || strain: Ka4C1 || sample_title: B. xylophilus mixed-stage || description: B.xylophilus mixed-stage on B. cinerea || sample_name: BxMixed || bioproject_id: PRJDB3458 || dev_stage: mixed propagative@�� DRP002612DRP002612Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.@�� DRA002992MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11
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/^ �L��lP ! )I �Q 3 W � ]�W �W O 3@��@ DRR029458DRR0294582017-04-13Ak5r� A�x,Y DRX026518@�C DRX026518DRX026518Illumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002611DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�d� DRS019416DRS019416�sex: mix || strain: Ka4C1 || sample_title: B.xylophilus cont Aug || description: B.xylophilus control in August || sample_name: BxContAug || bioproject_id: PRJDB3458 || dev_stage: mixed propagative@�� DRP002611DRP002611Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.@�� DRA002997MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11�L��kP ! )I �Q 3 W � ]�W �W O 3@�� DRR029457DRR0294572017-06-19Ae>� A��j@ DRX026517@�B� DRX026517DRX026517Illumina HiSeq 2000 paired end sequencing of SAMD00025065DRP002610DRS019416RNA-SeqTRANSCRIPTOMICRANDOMPAIRED - NOMINAL_LENGTH: 300; READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 102ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�d� DRS019416DRS019416�sex: mix || strain: Ka4C1 || sample_title: B.xylophilus cont Aug || description: B.xylophilus control in August || sample_name: BxContAug || bioproject_id: PRJDB3458 || dev_stage: mixed propagative@�� DRP002610DRP002610Bursaphelenchus xylophilus transcriptomeOtherTranscriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.Transcriptome analysis of several stages/conditions of the pine wood nematode Bursaphelenchus xylophilus. Stages contain egg, 2nd stage larva, 3rd stage larva, 4th stage larva, adult female, adult male, dauer 3rd stage juvenile, dauer 3rd stage juvenile, mixed-stage and mixed-stage infected.@�� DRA002996MIYAZAKIParasitology, Faculty of Medicine2018-05-10 18:11:11
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9r �B��$P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034261DRR0342612015-05-01AUg\� A�]� DRX030894@�� DRX030894DRX030894Illumina HiSeq 2000 sequencing of SAMD00029596DRP002638DRS019576LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019576DRS019576�sample_title: LL tomato Time32 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL32 shows 32 hours later with the light. || sample_name: LL32 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��#P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034269DRR0342692015-05-01A4�� A���� DRX030902@�� DRX030902DRX030902Illumina HiSeq 2000 sequencing of SAMD00029605DRP002638DRS019585LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@� DRS019585DRS019585�sample_title: LL tomato Time48 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL48 shows 48 hours later with the light. || sample_name: LL48 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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=v �B��&P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034262DRR0342622015-05-01AJ�e A�]D| DRX030895@� DRX030895DRX030895Illumina HiSeq 2000 sequencing of SAMD00029597DRP002638DRS019577LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@� DRS019577DRS019577�sample_title: LL tomato Time34 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL34 shows 34 hours later with the light. || sample_name: LL34 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�>��%P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034246DRR0342462015-05-01AQ@ A�N
� DRX030879@� DRX030879DRX030879Illumina HiSeq 2000 sequencing of SAMD00029589DRP002638DRS019569LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019569DRS019569�sample_title: LL tomato Time2 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL2 shows 2 hours later with the light. || sample_name: LL2 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��(P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034256DRR0342562015-05-01AQi� A���8 DRX030889@�� DRX030889DRX030889Illumina HiSeq 2000 sequencing of SAMD00029591DRP002638DRS019571LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019571DRS019571�sample_title: LL tomato Time22 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL22 shows 22 hours later with the light. || sample_name: LL22 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��'P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034259DRR0342592015-05-01AF$Հ A��Z" DRX030892@�@ DRX030892DRX030892Illumina HiSeq 2000 sequencing of SAMD00029594DRP002638DRS019574LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�@ DRS019574DRS019574�sample_title: LL tomato Time28 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL28 shows 28 hours later with the light. || sample_name: LL28 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��*P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034271DRR0342712015-05-01AQ|� A�ݧ, DRX030904@�@ DRX030904DRX030904Illumina HiSeq 2000 sequencing of SAMD00029607DRP002638DRS019587LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019587DRS019587�sample_title: LL tomato Time52 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL52 shows 52 hours later with the light. || sample_name: LL52 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��)P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034266DRR0342662015-05-01AS� A�f0 DRX030899@� DRX030899DRX030899Illumina HiSeq 2000 sequencing of SAMD00029602DRP002638DRS019582LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�@ DRS019582DRS019582�sample_title: LL tomato Time42 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL42 shows 42 hours later with the light. || sample_name: LL42 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9v �>��,P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034249DRR0342492015-05-01A3%; A��V DRX030882@�� DRX030882DRX030882Illumina HiSeq 2000 sequencing of SAMD00029618DRP002638DRS019598LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�@ DRS019598DRS019598�sample_title: LL tomato Time8 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL8 shows 8 hours later with the light. || sample_name: LL8 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��+P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034268DRR0342682015-05-01A@� A�T� DRX030901@�� DRX030901DRX030901Illumina HiSeq 2000 sequencing of SAMD00029604DRP002638DRS019584LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019584DRS019584�sample_title: LL tomato Time46 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL46 shows 46 hours later with the light. || sample_name: LL46 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��.P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034257DRR0342572015-05-01AC�� A�&�� DRX030890@�� DRX030890DRX030890Illumina HiSeq 2000 sequencing of SAMD00029592DRP002638DRS019572LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019572DRS019572�sample_title: LL tomato Time24 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL24 shows 24 hours later with the light. || sample_name: LL24 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��-P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034252DRR0342522015-05-01AI� A��� DRX030885@�� DRX030885DRX030885Illumina HiSeq 2000 sequencing of SAMD00029586DRP002638DRS019566LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@��@ DRS019566DRS019566�sample_title: LL tomato Time14 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL14 shows 14 hours later with the light. || sample_name: LL14 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��0P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034250DRR0342502015-05-01Am Ah>�` DRX030883@� DRX030883DRX030883Illumina HiSeq 2000 sequencing of SAMD00029584DRP002638DRS019564LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019564DRS019564�sample_title: LL tomato Time10 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL10 shows 10 hours later with the light. || sample_name: LL10 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��/P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034255DRR0342552015-05-01AP��@ A��c� DRX030888@�@ DRX030888DRX030888Illumina HiSeq 2000 sequencing of SAMD00029590DRP002638DRS019570LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@��@ DRS019570DRS019570�sample_title: LL tomato Time20 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL20 shows 20 hours later with the light. || sample_name: LL20 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��2P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034267DRR0342672015-05-01APl� A�-6� DRX030900@�@ DRX030900DRX030900Illumina HiSeq 2000 sequencing of SAMD00029603DRP002638DRS019583LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019583DRS019583�sample_title: LL tomato Time44 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL44 shows 44 hours later with the light. || sample_name: LL44 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��1P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034253DRR0342532015-05-01AP��@ A�
� DRX030886@�� DRX030886DRX030886Illumina HiSeq 2000 sequencing of SAMD00029587DRP002638DRS019567LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019567DRS019567�sample_title: LL tomato Time16 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL16 shows 16 hours later with the light. || sample_name: LL16 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��4P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034260DRR0342602015-05-01AB��� A��jt DRX030893@�� DRX030893DRX030893Illumina HiSeq 2000 sequencing of SAMD00029595DRP002638DRS019575LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019575DRS019575�sample_title: LL tomato Time30 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL30 shows 30 hours later with the light. || sample_name: LL30 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��3P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034254DRR0342542015-05-01AU�L� A�q�) DRX030887@� DRX030887DRX030887Illumina HiSeq 2000 sequencing of SAMD00029588DRP002638DRS019568LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019568DRS019568�sample_title: LL tomato Time18 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL18 shows 18 hours later with the light. || sample_name: LL18 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9v �>��6P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034247DRR0342472015-05-01A@�� A�NrX DRX030880@�@ DRX030880DRX030880Illumina HiSeq 2000 sequencing of SAMD00029600DRP002638DRS019580LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019580DRS019580�sample_title: LL tomato Time4 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL4 shows 4 hours later with the light. || sample_name: LL4 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��5P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034258DRR0342582015-05-01AK � A��+� DRX030891@� DRX030891DRX030891Illumina HiSeq 2000 sequencing of SAMD00029593DRP002638DRS019573LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@� DRS019573DRS019573�sample_title: LL tomato Time26 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL26 shows 26 hours later with the light. || sample_name: LL26 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��8P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034277DRR0342772015-05-01AA�r A���� DRX030910@�� DRX030910DRX030910Illumina HiSeq 2000 sequencing of SAMD00029614DRP002638DRS019594LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�@ DRS019594DRS019594�sample_title: LL tomato Time64 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL64 shows 64 hours later with the light. || sample_name: LL64 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��7P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034264DRR0342642015-05-01AT5@ A��o DRX030897@�� DRX030897DRX030897Illumina HiSeq 2000 sequencing of SAMD00029599DRP002638DRS019579LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019579DRS019579�sample_title: LL tomato Time38 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL38 shows 38 hours later with the light. || sample_name: LL38 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��:P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034280DRR0342802015-05-01ACj�� A��zt DRX030913@�� DRX030913DRX030913Illumina HiSeq 2000 sequencing of SAMD00029617DRP002638DRS019597LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@� DRS019597DRS019597�sample_title: LL tomato Time70 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL70 shows 70 hours later with the light. || sample_name: LL70 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��9P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034272DRR0342722015-05-01AR�@ A���� DRX030905@�� DRX030905DRX030905Illumina HiSeq 2000 sequencing of SAMD00029608DRP002638DRS019588LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019588DRS019588�sample_title: LL tomato Time54 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL54 shows 54 hours later with the light. || sample_name: LL54 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��<P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034251DRR0342512015-05-01AI p A��@ DRX030884@�@ DRX030884DRX030884Illumina HiSeq 2000 sequencing of SAMD00029585DRP002638DRS019565LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019565DRS019565�sample_title: LL tomato Time12 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL12 shows 12 hours later with the light. || sample_name: LL12 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��;P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034279DRR0342792015-05-01AJ
�� A��g* DRX030912@�@ DRX030912DRX030912Illumina HiSeq 2000 sequencing of SAMD00029616DRP002638DRS019596LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019596DRS019596�sample_title: LL tomato Time68 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL68 shows 68 hours later with the light. || sample_name: LL68 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��>P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034275DRR0342752015-05-01A3�j A��� DRX030908@�@ DRX030908DRX030908Illumina HiSeq 2000 sequencing of SAMD00029612DRP002638DRS019592LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019592DRS019592�sample_title: LL tomato Time60 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL60 shows 60 hours later with the light. || sample_name: LL60 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��=P ! i )- �) 3 W � a9�E5�? !U 3@��@ DRR034263DRR0342632015-05-01AW
,� A�\v DRX030896@�@ DRX030896DRX030896Illumina HiSeq 2000 sequencing of SAMD00029598DRP002638DRS019578LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�@ DRS019578DRS019578�sample_title: LL tomato Time36 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL36 shows 36 hours later with the light. || sample_name: LL36 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��@P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034278DRR0342782015-05-01AA?� A�}�� DRX030911@� DRX030911DRX030911Illumina HiSeq 2000 sequencing of SAMD00029615DRP002638DRS019595LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019595DRS019595�sample_title: LL tomato Time66 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL64 shows 64 hours later with the light. || sample_name: LL66 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��?P ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034276DRR0342762015-05-01AT� � A�u�* DRX030909@�� DRX030909DRX030909Illumina HiSeq 2000 sequencing of SAMD00029613DRP002638DRS019593LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@� DRS019593DRS019593�sample_title: LL tomato Time62 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL62 shows 62 hours later with the light. || sample_name: LL62 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9v �>��BP ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034248DRR0342482015-05-01AG{U A��G� DRX030881@�� DRX030881DRX030881Illumina HiSeq 2000 sequencing of SAMD00029611DRP002638DRS019591LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019591DRS019591�sample_title: LL tomato Time6 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL6 shows 6 hours later with the light. || sample_name: LL6 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��AP ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034270DRR0342702015-05-01ALV? A���4 DRX030903@� DRX030903DRX030903Illumina HiSeq 2000 sequencing of SAMD00029606DRP002638DRS019586LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�@ DRS019586DRS019586�sample_title: LL tomato Time50 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL50 shows 50 hours later with the light. || sample_name: LL50 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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@y �B��DP ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034273DRR0342732015-05-01AF;� A���� DRX030906@�� DRX030906DRX030906Illumina HiSeq 2000 sequencing of SAMD00029609DRP002638DRS019589LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@� DRS019589DRS019589�sample_title: LL tomato Time56 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL56 shows 56 hours later with the light. || sample_name: LL56 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�;��CP ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034245DRR0342452015-05-01A`�G A�![ DRX030878@�� DRX030878DRX030878Illumina HiSeq 2000 sequencing of SAMD00029583DRP002638DRS019563LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�� DRS019563DRS019563�sample_title: LL tomato Time0 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL0 shows the moment with the light. || sample_name: LL0 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
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9r �B��FP ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034265DRR0342652015-05-01A2� A��ax DRX030898@�� DRX030898DRX030898Illumina HiSeq 2000 sequencing of SAMD00029601DRP002638DRS019581LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@� DRS019581DRS019581�sample_title: LL tomato Time40 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL40 shows 40 hours later with the light. || sample_name: LL40 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11�B��EP ! i )- �) 3 W � a9�E5�? !U 3@�� DRR034274DRR0342742015-05-01AN�� A���, DRX030907@� DRX030907DRX030907Illumina HiSeq 2000 sequencing of SAMD00029610DRP002638DRS019590LL tomatoRNA-SeqTRANSCRIPTOMICHybrid SelectionSINGLE - READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000@�@ DRS019590DRS019590�sample_title: LL tomato Time58 || tissue_type: leaf || description: The tomato was grown in a fully controlled plant factory using a deep flow technique hydroponic system and continuous light [250-450 micromol m^2 s^1 (PPFD)].The samples were collected every two hours.LL58 shows 58 hours later with the light. || sample_name: LL58 || bioproject_id: PRJDB3891 || cultivar: Taian-kichijitsu@� DRP002638DRP002638RNAseq in a fully controlled plant factoryTranscriptome AnalysisTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a fully controlled plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.Solanum lycopersicumTranscriptome data of the tomato cultivar (Taian-kichijitsu) in a sunlight-type plant factory. The cultivar Taian-kichijitsu was grown in a fully controlled plant factory using a deep flow technique hydroponic system.@�& DRA003528OSAKA_PREFBioproduction Engineering Laboratory2018-05-10 18:11:11
�j�� S M !oE E G!}G/ �- �) C g �S} �C �9! G G�m�O + 3@�I@ E-MTAB-387:Early_Exponential.txtERR0196522016-06-28AX��@ A��8� Genomics Core Facility, EMBL, Heidelberg, GermanyE-MTAB-387:Early_Exponential@�@ E-MTAB-387:Early_ExponentialERX007970RNA sequencing in E. coli K12E-MTAB-387E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Early_exponentialRNA sequencing in E. coli K12Early_ExponentialOTHEROTHERcDNASINGLE - The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: GENOTYPE: wide_type || Experimental Factor: GROWTHCONDITION: early-exponential@拠 E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Early_exponentialERS0161162Protocols: The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).Organism: Escherichia coli || StrainOrLine: K-12 substr. MG1655 || Genotype: wide_type@�� E-MTAB-387ERP000350RNA sequencing in E. coli K12OtherRNA sequencing in E. coli K12Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phaseE-MTAB-387 in ArrayExpress: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MTAB-387@�G� ERA014184EMBL_HeidelbergEBI2018-05-10 18:11:11
� � �#�� U [ !oS S G!� G= �- �) C g �m� �C �9! G G�m�O + 3@�I` E-MTAB-387:Transition_to_Stationary.txtERR0196532016-06-28A[2u@ A���� Genomics Core Facility, EMBL, Heidelberg, GermanyE-MTAB-387:Transition_to_Stationary@� E-MTAB-387:Transition_to_StationaryERX007969RNA sequencing in E. coli K12E-MTAB-387E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationaryRNA sequencing in E. coli K12Transition_to_StationaryOTHEROTHERcDNASINGLE - The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: GENOTYPE: wide_type || Experimental Factor: GROWTHCONDITION: transition-to-stationary-phase@拀 E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationaryERS0161152Protocols: The E. coliK-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37¡C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80¡C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).Organism: Escherichia coli || StrainOrLine: K-12 substr. MG1655 || Genotype: wide_type@�� E-MTAB-387ERP000350RNA sequencing in E. coli K12OtherRNA sequencing in E. coli K12Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phaseE-MTAB-387 in ArrayExpress: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MTAB-387@�G� ERA014184EMBL_HeidelbergEBI2018-05-10 18:11:11 both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber cortex@�` E-MTAB-552:Tuber cortexERS023602Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber cortex || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11
h � ��� h � ��dV ; !C- - �S!7�) � �) C g g7 �' �9! �9 ���5 1 3@� E-MTAB-552:RHs13.txt.gzERR0299212016-08-09Ab\p� A���� Aalborg University, DenmarkE-MTAB-552:RHs13@�� E-MTAB-552:RHs13ERX010649Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Tuber peelTranscriptome Analysis of the potato (genotype RH89-039-16)S13WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurr 2�M��cW ; !C- - �M!;�) � �) = a �C; �' �k! �9 ���5 1 3@�0 E-MTAB-552:RHs08.txt.gzERR0299162016-08-09AX M� A� Wx Aalborg University, DenmarkE-MTAB-552:RHs08@�` E-MTAB-552:RHs08ERX010637Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Mature TuberTranscriptome Analysis of the potato (genotype RH89-039-16)S8WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested 1�{��bV ; !C- - �S!/�) � �) C g _/ �' �1! �9 ���5 1 3@�P E-MTAB-552:RHs10.txt.gzERR0299182016-08-09Ag P A���$ Aalborg University, DenmarkE-MTAB-552:RHs10@� E-MTAB-552:RHs10ERX010642Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:StamenTranscriptome Analysis of the potato (genotype RH89-039-16)S10WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, ant 0�q��aV ; !C- - �M!/�) � �) = a _/ �' �1! �9 ���5 1 3@� E-MTAB-552:RHs01.txt.gzERR0299092016-08-09AWf.� A�R�P Aalborg University, DenmarkE-MTAB-552:RHs01@� E-MTAB-552:RHs01ERX010643Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:FlowerTranscriptome Analysis of the potato (genotype RH89-039-16)S1WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same tim /���`V ; !C- - �S!;�) � �) C g k; �' �=! �9 ���5 1 3@� E-MTAB-552:RHs16.txt.gzERR0299242016-08-09Ae�� A�7� Aalborg University, DenmarkE-MTAB-552:RHs16@秀 E-MTAB-552:RHs16ERX010646Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Tuber cortexTranscriptome Analysis of the potato (genotype RH89-039-16)S16WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and - e, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: flower@� E-MTAB-552:FlowerERS023599Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: flower || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 hesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: stamen@�� E-MTAB-552:StamenERS023598Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stamen || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: tuber || Experimental Factor: DEVELOPMENTALSTAGE: mature@�@ E-MTAB-552:Mature TuberERS023593Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber || DevelopmentalStage: mature || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 ed and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber peel@� E-MTAB-552:Tuber peelERS023605Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber peel || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 me time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: stem@� E-MTAB-552:StemERS023607Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stem || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11
�
�� � �u��iV ; !C- - �M!1�) � �) = a a1 �' �3! �9 ���5 1 3@�� E-MTAB-552:RHs03.txt.gzERR0299112016-08-09AX�E� A��x Aalborg University, DenmarkE-MTAB-552:RHs03@�` E-MTAB-552:RHs03ERX010645Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:PetioleTranscriptome Analysis of the potato (genotype RH89-039-16)S3WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, 8���hV ; !C- - �S!;�) � �) C g k; �' �=! �9 ���5 1 3@� E-MTAB-552:RHs15.txt.gzERR0299232016-08-09Ae�^ A�r� Aalborg University, DenmarkE-MTAB-552:RHs15@禀 E-MTAB-552:RHs15ERX010638Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Tuber sproutTranscriptome Analysis of the potato (genotype RH89-039-16)S15WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and 7� ��gV ; !C- - �S!7�) � �) C g g7 �' �9! �9 ���5 1 3@�p E-MTAB-552:RHs12.txt.gzERR0299202016-08-09Ag>� A�&�� Aalborg University, DenmarkE-MTAB-552:RHs12@� E-MTAB-552:RHs12ERX010640Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Tuber pithTranscriptome Analysis of the potato (genotype RH89-039-16)S12WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurr 6�r��fV ; !C- - �S!+�) � �) C g [+ �' �-! �9 ���5 1 3@�@ E-MTAB-552:RHs09.txt.gzERR0299172016-08-09AgI�` A�2�� Aalborg University, DenmarkE-MTAB-552:RHs09@秠 E-MTAB-552:RHs09ERX010647Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:RootTranscriptome Analysis of the potato (genotype RH89-039-16)S9WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same tim 5�i��eV ; !C- - �M!+�) � �) = a [+ �' �-! �9 ���5 1 3@� E-MTAB-552:RHs05.txt.gzERR0299132016-08-09AW� A��0� Aalborg University, DenmarkE-MTAB-552:RHs05@� E-MTAB-552:RHs05ERX010651Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:StemTranscriptome Analysis of the potato (genotype RH89-039-16)S5WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the sa 3 e, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: root@� E-MTAB-552:RootERS023603Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: root || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 ed and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber pith@� E-MTAB-552:Tuber pithERS023596Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber pith || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: tuber sprout@�` E-MTAB-552:Tuber sproutERS023594Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber sprout || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: petiole@�@ E-MTAB-552:PetioleERS023601Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: petiole || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 ed (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: tuber || Experimental Factor: DEVELOPMENTALSTAGE: young@� E-MTAB-552:Young TuberERS023595Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: tuber || DevelopmentalStage: young || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11
Q � ��� Q �J��nW ; !C- - �S!I�) � �) C g �KI �' �-! �9 ���5 1 3@�` E-MTAB-552:RHs11.txt.gzERR0299192016-08-09Agl� A�Ze� Aalborg University, DenmarkE-MTAB-552:RHs11@� E-MTAB-552:RHs11ERX010648Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Water stressed leafTranscriptome Analysis of the potato (genotype RH89-039-16)S11WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds w >�q��mV ; !C- - �M!/�) � �) = a _/ �' �1! �9 ���5 1 3@� E-MTAB-552:RHs06.txt.gzERR0299142016-08-09AYO
A�x� Aalborg University, DenmarkE-MTAB-552:RHs06@�@ E-MTAB-552:RHs06ERX010644Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:StolonTranscriptome Analysis of the potato (genotype RH89-039-16)S6WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same tim =�i��lV ; !C- - �M!+�) � �) = a [+ �' �-! �9 ���5 1 3@�� E-MTAB-552:RHs02.txt.gzERR0299102016-08-09AY�� A��%� Aalborg University, DenmarkE-MTAB-552:RHs02@�� E-MTAB-552:RHs02ERX010641Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:LeafTranscriptome Analysis of the potato (genotype RH89-039-16)S2WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the sa <���kV ; !C- - �M!7�) � �) = a g7 �' �9! �9 ���5 1 3@�� E-MTAB-552:RHs04.txt.gzERR0299122016-08-09AW#ր A�QP Aalborg University, DenmarkE-MTAB-552:RHs04@� E-MTAB-552:RHs04ERX010650Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Shoot apexTranscriptome Analysis of the potato (genotype RH89-039-16)S4WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis ;�I��jW ; !C- - �M!9�) � �) = a �A9 �' �i! �9 ���5 1 3@� E-MTAB-552:RHs07.txt.gzERR0299152016-08-09AX4� A�;A� Aalborg University, DenmarkE-MTAB-552:RHs07@禠 E-MTAB-552:RHs07ERX010639Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Young TuberTranscriptome Analysis of the potato (genotype RH89-039-16)S7WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvest 9 occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: shoot apex@�� E-MTAB-552:Shoot apexERS023606Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: shoot apex || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 me time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: leaf@� E-MTAB-552:LeafERS023597Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: leaf || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 e, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome AnalyzerINSTRUMENT_MODEL: Illumina Genome AnalyzerExperimental Factor: ORGANISMPART: stolon@� E-MTAB-552:StolonERS023600Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: stolon || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 ere harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: leaf || Experimental Factor: GROWTHCONDITION: water stressed@� E-MTAB-552:Water stressed leafERS023604Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: leaf || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11 sted (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNaseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: ORGANISMPART: whole plant || Experimental Factor: GROWTHCONDITION: in vitro@� E-MTAB-552:Whole in vitro plantERS023608Protocols: RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested. A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.Organism: Solanum tuberosum || OrganismPart: whole plant || BioSourceType: fresh_sample@�� E-MTAB-552ERP000527Transcriptome Analysis of the potato (genotype RH89-039-16)Transcriptome AnalysisTranscriptome Analysis of the potato (genotype RH89-039-16)Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-552@�f ERA021569AAUAalborg University2018-05-10 18:11:11
� � � �T��>R A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3@�GP E-MTAB-861:21days.fastq.gzERR0564802016-06-28@�� A+�� GATC BIOTECH AGE-MTAB-861:assay 4@ E-MTAB-861:assay 4ERX033523wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 4wheat starchy endosperm RNA-SeqRNA Extract 4RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 21 d@�p E-MTAB-861:Central starchy endosperm 4ERS074999�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 21 d || OrganismPart: starchy endosperm@�Z E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861@��� ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11�T��oW ; !C- - �S!K�) � �) C g �MK �' �;! �9 ���5 1 3@� E-MTAB-552:RHs14.txt.gzERR0299222016-08-09A_�� A�� @ Aalborg University, DenmarkE-MTAB-552:RHs14@�@ E-MTAB-552:RHs14ERX010652Illumina Genome Analyzer II sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)E-MTAB-552E-MTAB-552:Whole in vitro plantTranscriptome Analysis of the potato (genotype RH89-039-16)S14WGSTRANSCRIPTOMICRANDOMSINGLE - RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harve ?
' ' �T��?R A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3@�G@ E-MTAB-861:17days.fastq.gzERR0564792016-06-28@� A(Ԗ GATC BIOTECH AGE-MTAB-861:assay 3@� E-MTAB-861:assay 3ERX033527wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 3wheat starchy endosperm RNA-SeqRNA Extract 3RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 17 d@�� E-MTAB-861:Central starchy endosperm 3ERS075003�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 17 d || OrganismPart: starchy endosperm@�Z E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861@��� ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11
' ' �T��@R A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3@�G` E-MTAB-861:28days.fastq.gzERR0564812016-06-28@�� A/2� GATC BIOTECH AGE-MTAB-861:assay 5@� E-MTAB-861:assay 5ERX033525wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 5wheat starchy endosperm RNA-SeqRNA Extract 5RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 28 d@�� E-MTAB-861:Central starchy endosperm 5ERS075001�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 28 d || OrganismPart: starchy endosperm@�Z E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861@��� ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11
' ' �T��AR A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3@�G E-MTAB-861:10days.fastq.gzERR0564772016-06-28@�|@ A6 � GATC BIOTECH AGE-MTAB-861:assay 1@�� E-MTAB-861:assay 1ERX033526wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 1wheat starchy endosperm RNA-SeqRNA Extract 1RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 10 d@�� E-MTAB-861:Central starchy endosperm 1ERS075002�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 10 d || OrganismPart: starchy endosperm@�Z E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861@��� ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11
' ' �T��BR A !+1 1 K!YK') �A �) C g IY �W �_! K K��5 +3 3@�G0 E-MTAB-861:14days.fastq.gzERR0564782016-06-28@� A+(` GATC BIOTECH AGE-MTAB-861:assay 2@ E-MTAB-861:assay 2ERX033524wheat starchy endosperm RNA-SeqE-MTAB-861E-MTAB-861:Central starchy endosperm 2wheat starchy endosperm RNA-SeqRNA Extract 2RNA-SeqTRANSCRIPTOMICcDNASINGLE - Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIExperimental Factor: Age: 14 d@�� E-MTAB-861:Central starchy endosperm 2ERS075000�Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 14 d || OrganismPart: starchy endosperm@�Z E-MTAB-861ERP001030wheat starchy endosperm RNA-SeqOtherwheat starchy endosperm RNA-SeqTranscriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861@��� ERA070843GATC Biotech AGRothamsted Research2018-05-10 18:11:11
@ @ �;��$V = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3A0` E-MTAB-1585:7sk_1b.fq.gzERR2474162016-06-28An� AȡQA� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_1bA4� E-MTAB-1585:7sk_1bERX221956Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_1bTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_1bRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneA p E-MTAB-1585:7sk_1bERS225457'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)A X E-MTAB-1585:7sk_6cERS225454'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
�j��&W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0� E-MTAB-1585:7sk_6a.fq.gzERR2474212016-06-28AeG A�� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_6aA4� E-MTAB-1585:7sk_6aERX221947Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_6aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_6aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin H�j��%W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0@ E-MTAB-1585:7sk_6c.fq.gzERR2474122016-06-28A��8 A�%F� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_6cA4� E-MTAB-1585:7sk_6cERX221953Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_6cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_6cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin F g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)A ( E-MTAB-1585:7sk_6aERS225448'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
@ @ �;��'V = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3A08 E-MTAB-1585:7sk_1a.fq.gzERR2474112016-06-28Ap� Aʋ]� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_1aA4� E-MTAB-1585:7sk_1aERX221952Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_1aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_1aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneA P E-MTAB-1585:7sk_1aERS225453'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)A H E-MTAB-1585:7sk_2cERS225452'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
�j��)W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0x E-MTAB-1585:7sk_2b.fq.gzERR2474192016-06-28AmX� A�b. � ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_2bA4� E-MTAB-1585:7sk_2bERX221957Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_2bTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_2bRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin L�j��(W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0h E-MTAB-1585:7sk_2c.fq.gzERR2474172016-06-28A��hX A��fL@ ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_2cA4� E-MTAB-1585:7sk_2cERX221951Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_2cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_2cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin J g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)A x E-MTAB-1585:7sk_2bERS225458'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
@ @ �;��*V = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3A00 E-MTAB-1585:7sk_4a.fq.gzERR2474102016-06-28AR�� A��� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_4aA4� E-MTAB-1585:7sk_4aERX221948Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_4aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_4aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneA 0 E-MTAB-1585:7sk_4aERS225449'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
@ @ �;��+V = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3A0H E-MTAB-1585:7sk_1c.fq.gzERR2474132016-06-28A��` A���܀ ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_1cA4p E-MTAB-1585:7sk_1cERX221945Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_1cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_1cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneA E-MTAB-1585:7sk_1cERS225446'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)A h E-MTAB-1585:7sk_2aERS225456'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
8
*8 �j��/W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0P E-MTAB-1585:7sk_5a.fq.gzERR2474142016-06-28AS�2� A�u�| ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_5aA4x E-MTAB-1585:7sk_5aERX221946Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_5aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_5aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin S�j��.W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0� E-MTAB-1585:7sk_3a.fq.gzERR2474202016-06-28AZ�= A�]$� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_3aA4h E-MTAB-1585:7sk_3aERX221944Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_3aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_3aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin R�j��-W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0p E-MTAB-1585:7sk_3c.fq.gzERR2474182016-06-28Ar�GP A��!�� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_3cA4� E-MTAB-1585:7sk_3cERX221954Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_3cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_3cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin Q�j��,W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0� E-MTAB-1585:7sk_2a.fq.gzERR2474232016-06-28Aid�� A�<c2� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_2aA4� E-MTAB-1585:7sk_2aERX221955Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_2aTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_2aRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin O g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)A ` E-MTAB-1585:7sk_3cERS225455'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (3' ASO)A E-MTAB-1585:7sk_3aERS225445'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)A E-MTAB-1585:7sk_5aERS225447'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
@ @ �;��0V = !91 1 � #1� ) �s 3 W k1 � �M# � �i� �i�9 % 3A0X E-MTAB-1585:7sk_4c.fq.gzERR2474152016-06-28AtG�� A�) ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_4cA4� E-MTAB-1585:7sk_4cERX221949Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_4cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_4cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: noneA 8 E-MTAB-1585:7sk_4cERS225450'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11 g et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000Experimental Factor: genetic modification: Knockdown (5' ASO)A @ E-MTAB-1585:7sk_5cERS225451'jProtocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza). Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal@�� E-MTAB-1585ERP002405Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsOtherTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsTranscriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585@�[` ERA203799EMBL-EBIArrayExpress2018-05-10 18:11:11
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M = !! = = A / ) ' �) # G / % /%]] 5 3AS8 run_AIG_AOSS_7_42RALAAXXERR2603762009-09-212016-06-28Apʺ� A��x Genoscopeexp_AIG_AOSS_7_42RALAAXXAW exp_AIG_AOSS_7_42RALAAXXERX234948Adineta vaga GA IIx Simplestudy_AIGsample_AIG_104782AIGAOSSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none providedREAD_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1ILLUMINAunspecifiedINSTRUMENT_MODEL: unspecifiedA sample_AIG_104782ERS235800�NAdineta vaga@� study_AIGERP002474Adineta_vaga_cdnaMetagenomicsTranscriptome sequencing of Adineta vagaAIGTranscriptome sequencing of Adineta vagaLinked publication: http://dx.doi.org/10.1038/nature12326@��p ERA206999GSCThe Genoscope center2018-05-10 18:11:11�f�� M E !! E E E / ) ' �I3 W / % /%]] 5 3AS@ run_1.GAC.AIG_AOTS_GWDJGJ101ERR2603772011-01-202016-06-28A�< A�h�V Genoscopeexp_1.GAC.AIG_AOTS_GWDJGJ101AW exp_1.GAC.AIG_AOTS_GWDJGJ101ERX234949Adineta vaga Titanium Simplestudy_AIGsample_AIG_104782AIGAOTSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none providedREAD_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX TitaniumA sample_AIG_104782ERS235800�NAdineta vaga@� study_AIGERP002474Adineta_vaga_cdnaMetagenomicsTranscriptome sequencing of Adineta vagaAIGTranscriptome sequencing of Adineta vagaLinked publication: http://dx.doi.org/10.1038/nature12326@��p ERA206999GSCThe Genoscope center2018-05-10 18:11:11�f��M E !! E E E / ) ' �I3 W / % /%]] 5 3ASH run_2.GAC.AIG_AOTS_GWDJGJ102ERR2603782011-01-202016-06-28A�� A� A� Genoscopeexp_2.GAC.AIG_AOTS_GWDJGJ102AW exp_2.GAC.AIG_AOTS_GWDJGJ102ERX234950Adineta vaga Titanium Simplestudy_AIGsample_AIG_104782AIGAOTSRNA-SeqTRANSCRIPTOMICcDNASINGLE - none providedREAD_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLX TitaniumINSTRUMENT_MODEL: 454 GS FLX TitaniumA sample_AIG_104782ERS235800�NAdineta vaga@� study_AIGERP002474Adineta_vaga_cdnaMetagenomicsTranscriptome sequencing of Adineta vagaAIGTranscriptome sequencing of Adineta vagaLinked publication: http://dx.doi.org/10.1038/nature12326@��p ERA206999GSCThe Genoscope center2018-05-10 18:11:11�j��1W = !91 1 � #1� ) � 3 W �1 �) �M# � �i� �i�9 % 3A0� E-MTAB-1585:7sk_5c.fq.gzERR2474222016-06-28Avz�� A��R� ROCKEFELLER UNIVERSITYE-MTAB-1585:7sk_5cA4� E-MTAB-1585:7sk_5cERX221950Transcriptional profiling of 7SK knockdown in mouse embryonic stem cellsE-MTAB-1585E-MTAB-1585:7sk_5cTranscriptional profiling of 7SK knockdown in mouse embryonic stem cells7sk_5cRNA-SeqTRANSCRIPTOMICRANDOMSINGLE - Oct4-GIP mouse embryonic stem (ES) cells (Yin U
j �j �FٺyP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUPZL4S01SRR0006562007-08-282013-07-25A
�� A��` WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�FٺxP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUEMSW407SRR0006502007-08-222013-07-25@�� A�t WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
j �j �Fٺ{P !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUEMSW402SRR0006542007-08-222013-07-25@�� A* WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�FٺzP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUEMSW403SRR0006532007-08-222013-07-25@�� A)�j WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
j �j �Fٺ}P !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUEMSW401SRR0006522007-08-222013-07-25@�t A\� WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�Fٺ|P !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUEMSW404SRR0006512007-08-222013-07-25@�� A2_o WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
j �j �FٺP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUGXWLM02SRR0006492007-08-232013-07-25A�� A��~x WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�Fٺ~P !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUPZL4S02SRR0006582007-08-282013-07-25A
�� A��|p WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
j �j �FٻP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUEMSW405SRR0006482007-08-222013-07-25@w� @��P WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�Fٻ P !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUEMSW406SRR0006572007-08-222013-07-25@�� A�x WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
j �j �FٻP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUGXWLM01SRR0006472007-08-232013-07-25A � A���H WUGSC2036533341flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036533341SRX000121454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036533341FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11�FٻP !!! �U! �9;O!) �I! E =9 ' 9 a{9 I � =!3A0w� EUEMSW408SRR0006552007-08-222013-07-25@�� A#�� WUGSC2036546523flow_count: 400 || submission_id: SRA000241 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2036546523SRX000122454 sequencing of Tachyglossus aculeatus transcript fragment library2036532902, 2036545831Tachyglossus aculeatus none provided 2036546523FL-cDNATRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000241A'�� Tachyglossus aculeatusSRS000290$-none provided@�=� 2036532902, 2036545831SRP000098Tachyglossus aculeatus Transcriptome StudyOtherTachyglossus aculeatus Transcriptome Sequencing ProjectTachyglossus aculeatusparent_bioproject: PRJNA167910A�` SRA000241Ftp submission of runfiles WUGSC.08232007.125222.81794080.3,WUGSC.08232007.125221.81794080.2,WUGSC.08232007.125228.81794080.7,WUGSC.08232007.125236.81794080.11,WUGSC.08232007.125238.81794080.12,WUGSC.08232007.125227.81794080.6,WUGSC.08232007.125219.81794080.1,WUGSC.08232007.125235.81794080.10,WUGSC.08262007.070409.81852896.2,WUGSC.08262007.070235.81852896.1,WUGSC.08292007.070434.81926184.2,WUGSC.08292007.070248.81926184.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-08-232018-05-10 18:11:11
� � �oٻU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3A0w� EXRHO8E06SRR0001422007-10-232013-01-31@� A(+F WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246A'�� 20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba@�@ 2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331A�t SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �oٻU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3A0w� EXRHO8E07SRR0001392007-10-232013-01-31@�� A4�A WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246A'�� 20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba@�@ 2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331A�t SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �oٻU !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3A0w� EZNCMKS01SRR0001412007-11-282013-01-31A }� A��� WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246A'�� 20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba@�@ 2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331A�t SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �oٻ U !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3A0w� EXRHO8E08SRR0001382007-10-232013-01-31@�W A4&� WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246A'�� 20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba@�@ 2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331A�t SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �oٻ U !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3A0w� EZNCMKS02SRR0001402007-11-282013-01-31A
�� A���p WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246A'�� 20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba@�@ 2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331A�t SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
� � �oٻ U !!! �U! �U!O! �I! E = �_� �! o;�k �+ G �=!3A0w� EXRHO8E05SRR0001372007-10-232013-01-31@�x A#I� WUGSC2140631529flow_count: 400 || submission_id: SRA000246 || flow_sequence: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG || key_sequence: TCAGA/�� 2140631529SRX000023454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library2140628333Streptococcus infantarius subsp. infantarius ATCC BAA-102 none provided 2140631529WGSGENOMICRANDOMSINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXsubmission_id: SRA000246A'�� 20527SRS0000173@Streptococcus infantarius (16S rDNA gene sequence is not available) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces.DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteriafinishing strategy (depth of coverage): Level 3: Improved-High-Quality Draft13.9x;29 || collection date: not determined || estimated_size: 1925000 || sop: http://hmpdacc.org/doc/CommonGeneAnnotation_SOP.pdf || project_type: Reference Genome || host: Homo sapiens || lat_lon: not determined || biome: terrestrial biome [ENVO:00000446] || misc_param: HMP body site: not determined || nucleic acid extraction: not determined || feature: human-associated habitat [ENVO:00009003] || investigation_type: missing || host taxid: 9606 || project_name: Streptococcus infantarius infantarius ATCC BAA-102 || assembly: Newbler, PCAP || geo_loc_name: not determined || source_mat_id: ATCC BAA-102, LMG 19578, CCUG 43820 || material: biological product [ENVO:02000043] || ref_biomaterial: not determined || misc_param: HMP supersite: gastrointestinal_tract || num_replicons: not determined || sequencing method: 454-GS20, Sanger || isol_growth_condt: not determined || env_package: missing || strain: ATCC BAA-102 || sub_species: infantarius || isolation-source: missing || BioSampleModel: MIGS.ba@�@ 2140628333SRP000017Reference genome for the Human Microbiome ProjectWhole Genome Sequencing<P><B><I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102</B>. <I>Streptococcus infantarius</I> subsp. <I>infantarius</I> ATCC BAA-102 was isolated from the feces from a healthy human infant. This is the type strain and is being sequenced as part of the human gut microbiome project.Streptococcus infantarius subsp. infantarius ATCC BAA-102GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364parent_bioproject: PRJNA28331A�t SRA000246Ftp submission of runfiles WUGSC.10252007.080547.83788500.12,WUGSC.10252007.080535.83788500.5,WUGSC.10252007.080529.83788500.2,WUGSC.10252007.080543.83788500.10,WUGSC.12182007.140854.85413372.2,WUGSC.12182007.140705.85413372.1 processed manually by shumwaym.WUGSCGenome Sequencing Center2007-10-252018-05-10 18:11:11
J %J �V��qS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.3SRR0182582014-06-09Am5�� A�F�: BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26770.0 || instrument_name: SL-XAN || lane: 3 || lsid: BROAD:SEQUENCING_SAMPLE:26770.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302A0� 30BV1AAXX080828-3-PSRX006124Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7010' containing sample 'M990514'Illumina sequencing of Homo sapiens via complementary DNASolexa-7010RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26770.0 || lsid: BROAD:SEQUENCING_SAMPLE:26770.0 || material_type: New Tech Library || project: G1681 || work_request: 17302A'� PRJNA39289.M990514SRS003455%�n/an/an/aSample name: M990514 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�V��pS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.7SRR0182612014-06-09An}` A��� BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26767.0 || instrument_name: SL-XAN || lane: 7 || lsid: BROAD:SEQUENCING_SAMPLE:26767.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302A0� 30BV1AAXX080828-7-PSRX006127Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7007' containing sample 'M980409'Illumina sequencing of Homo sapiens via complementary DNASolexa-7007RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26767.0 || lsid: BROAD:SEQUENCING_SAMPLE:26767.0 || material_type: New Tech Library || project: G1681 || work_request: 17302A'� PRJNA39289.M980409SRS003458%�n/an/an/aSample name: M980409 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
F #F �X��sS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.3SRR0182652014-06-09A_)K� A���* BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26765.0 || instrument_name: SL-XAN || lane: 3 || lsid: BROAD:SEQUENCING_SAMPLE:26765.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461A0� 30C3WAAXX080918-3-PSRX006131Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7005' containing sample 'M010403'Illumina sequencing of Homo sapiens via complementary DNASolexa-7005RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26765.0 || lsid: BROAD:SEQUENCING_SAMPLE:26765.0 || material_type: New Tech Library || project: G1681 || work_request: 17461A'� PRJNA39289.M010403SRS003460%�n/an/an/aSample name: M010403 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�X��rS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.6SRR0182672014-06-09Ak��` A��<� BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26774.0 || instrument_name: SL-XAN || lane: 6 || lsid: BROAD:SEQUENCING_SAMPLE:26774.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461A0� 30C3WAAXX080918-6-PSRX006133Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7014' containing sample 'M000921'Illumina sequencing of Homo sapiens via complementary DNASolexa-7014RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26774.0 || lsid: BROAD:SEQUENCING_SAMPLE:26774.0 || material_type: New Tech Library || project: G1681 || work_request: 17461A'� PRJNA39289.M000921SRS003462%�n/an/an/aSample name: M000921 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
J %J �V��uS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.8SRR0182622014-06-09Am�� A��� BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26766.0 || instrument_name: SL-XAN || lane: 8 || lsid: BROAD:SEQUENCING_SAMPLE:26766.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302A0� 30BV1AAXX080828-8-PSRX006128Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7006' containing sample 'M970109'Illumina sequencing of Homo sapiens via complementary DNASolexa-7006RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26766.0 || lsid: BROAD:SEQUENCING_SAMPLE:26766.0 || material_type: New Tech Library || project: G1681 || work_request: 17302A'� PRJNA39289.M970109SRS003459%�n/an/an/aSample name: M970109 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�V��tS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.6SRR0182602014-06-09An�6� A�k��� BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26768.0 || instrument_name: SL-XAN || lane: 6 || lsid: BROAD:SEQUENCING_SAMPLE:26768.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302A0� 30BV1AAXX080828-6-PSRX006126Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7008' containing sample 'M990802'Illumina sequencing of Homo sapiens via complementary DNASolexa-7008RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26768.0 || lsid: BROAD:SEQUENCING_SAMPLE:26768.0 || material_type: New Tech Library || project: G1681 || work_request: 17302A'� PRJNA39289.M990802SRS003457%�n/an/an/aSample name: M990802 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
R &R �O��wS � ! �!3 �a #)I �# C g �E+ � 9 C�y% I / 3A0�� BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.1SRR0182632014-06-09Ak,K� AէLC� BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 1 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17462A0� 30C3WAAXX080918-1-PSRX006129Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'Illumina sequencing of Homo sapiens via complementary DNASolexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17462A'� PRJNA39289.MEWOSRS003453%�n/an/an/aSample name: MEWO || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�U��vS � ! �!3 �g #)I �# C g �E1 � 9 C�y% I / 3A0�� BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.7SRR0182682014-06-09Am� � Aג
2� BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26775.0 || instrument_name: SL-XAN || lane: 7 || lsid: BROAD:SEQUENCING_SAMPLE:26775.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461A0� 30C3WAAXX080918-7-PSRX006134Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7015' containing sample 'K-562-4'Illumina sequencing of Homo sapiens via complementary DNASolexa-7015RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26775.0 || lsid: BROAD:SEQUENCING_SAMPLE:26775.0 || material_type: New Tech Library || project: G1681 || work_request: 17461A'� PRJNA39289.K-562-4SRS003463%�n/an/an/aSample name: K-562-4 || geographic location (country and/or sea,region): missing || isolation source: K-562 || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
H %H �X��yS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.5SRR0182662014-06-09AlVj� A֔� BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26773.0 || instrument_name: SL-XAN || lane: 5 || lsid: BROAD:SEQUENCING_SAMPLE:26773.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461A0� 30C3WAAXX080918-5-PSRX006132Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7013' containing sample '501 MEL'Illumina sequencing of Homo sapiens via complementary DNASolexa-7013RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26773.0 || lsid: BROAD:SEQUENCING_SAMPLE:26773.0 || material_type: New Tech Library || project: G1681 || work_request: 17461A'� PRJNA39289.501 MELSRS003461%�n/an/an/aSample name: 501 MEL || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�V��xS � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.5SRR0182592014-06-09Ajs�� A�?� BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26769.0 || instrument_name: SL-XAN || lane: 5 || lsid: BROAD:SEQUENCING_SAMPLE:26769.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302A0� 30BV1AAXX080828-5-PSRX006125Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7009' containing sample 'M000216'Illumina sequencing of Homo sapiens via complementary DNASolexa-7009RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26769.0 || lsid: BROAD:SEQUENCING_SAMPLE:26769.0 || material_type: New Tech Library || project: G1681 || work_request: 17302A'� PRJNA39289.M000216SRS003456%�n/an/an/aSample name: M000216 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
T .T �U��{S � ! �!3 �g #)I �# C g �E1 � 9 C�y% I / 3A0�� BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.8SRR0182692014-06-09An8q A��%� BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26776.0 || instrument_name: SL-XAN || lane: 8 || lsid: BROAD:SEQUENCING_SAMPLE:26776.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17461A0� 30C3WAAXX080918-8-PSRX006135Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7016' containing sample 'K-562-3'Illumina sequencing of Homo sapiens via complementary DNASolexa-7016RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 350; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26776.0 || lsid: BROAD:SEQUENCING_SAMPLE:26776.0 || material_type: New Tech Library || project: G1681 || work_request: 17461A'� PRJNA39289.K-562-3SRS003464%�n/an/an/aSample name: K-562-3 || geographic location (country and/or sea,region): missing || isolation source: K-562 || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�M��zS � ! �!3 �a #)I �# C g �E+ � 9 C�y% I / 3A0� BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.1SRR0182562014-06-09Ah�T� A��� BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 1 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302A0� 30BV1AAXX080828-1-PSRX006122Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'Illumina sequencing of Homo sapiens via complementary DNASolexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17302A'� PRJNA39289.MEWOSRS003453%�n/an/an/aSample name: MEWO || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11
Q %Q �O��}S � ! �!3 �a #)I �# C g �E+ � 9 C�y% I / 3A0�� BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.2SRR0182642014-06-09Al Ѐ A�P�& BIanalysis_type: cDNA || flowcell_barcode: 30C3WAAXX || gssr_id: 26772.0 || instrument_name: SL-XAN || lane: 2 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || project: G1681 || run_barcode: 30C3WAAXX080918 || run_name: 080918_SL-XAN_0001_FC30C3WAAXX || work_request: 17462A0� 30C3WAAXX080918-2-PSRX006130Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'Illumina sequencing of Homo sapiens via complementary DNASolexa-7012RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17462A'� PRJNA39289.MEWOSRS003453%�n/an/an/aSample name: MEWO || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11�V��|S � ! �!3 �g #)I �# C g �E1 �9 C�y% I / 3A0�� BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.2SRR0182572014-06-09Als ` A֫�܀ BIanalysis_type: cDNA || flowcell_barcode: 30BV1AAXX || gssr_id: 26771.0 || instrument_name: SL-XAN || lane: 2 || lsid: BROAD:SEQUENCING_SAMPLE:26771.0 || project: G1681 || run_barcode: 30BV1AAXX080828 || run_name: 080828_SL-XAN_0002_FC30BV1AAXX || work_request: 17302A0� 30BV1AAXX080828-2-PSRX006123Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7011' containing sample 'M980928'Illumina sequencing of Homo sapiens via complementary DNASolexa-7011RNA-SeqTRANSCRIPTOMICcDNAPAIRED - NOMINAL_LENGTH: 500; READ_INDEX: 0; READ_LABEL: forward; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1 || READ_INDEX: 1; READ_LABEL: reverse; READ_CLASS: Application Read; READ_TYPE: Reverse; BASE_COORD: 52ILLUMINAIllumina Genome Analyzer IIINSTRUMENT_MODEL: Illumina Genome Analyzer IIanalysis_type: cDNA || gssr_id: 26771.0 || lsid: BROAD:SEQUENCING_SAMPLE:26771.0 || material_type: New Tech Library || project: G1681 || work_request: 17302A'� PRJNA39289.M980928SRS003454%�n/an/an/aSample name: M980928 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing@��@ Melanoma_TranscriptomeSRP000931Melanoma Cell TranscriptomeOtherPaired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.Homo sapiensparent_bioproject: PRJNA118501A�8 SRA009053Produced by user prodinfo on Fri Mar 26 14:15:27 EDT 2010BIGenome Sequencing2018-05-10 18:11:11 rimer (5’CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGT3’), 25 µM Adapter B_For primer (5’CCTATCCCCTGTGTGCCTTGGCAGTCTCAGT3’), 3% DMSO, 10 mM dNTPs and 1 U Phusion polymerase (Finnzymes/NEB, USA). The PCR conditions were as follows: 980C for 30 seconds, followed by 15 cycles with 980C for 10 seconds, 680C for 30 seconds and 720C for 30 seconds, with a final extension of 720C for 5 minute and cleaned up with a Qiaquick minelute PCR column. Normalization of cDNA library The cDNA library was normalized according to the protocol described in the Trimmer Direct Kit (Evrogen, Russia). In brief, 300 ng of cDNA were incubated at 950C for 5 minutes followed by incubation at 680C for 4 hours in the hybridization buffer included in the kit (50 mM Hepes, pH7.5 and 0.5 M NaCl). After the incubation, the reaction was treated with ¼ units of duplex specific nuclease (DSN). The normalized cDNA was then amplified from 1 µl of DSN-treated cDNA by PCR reactions (10 cycles) described above and gel purified for the fragment size of 400-800 bp as described above.454ESTTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXA'�� double-haploid rainbow troutSRS004650 VTissues were collected from a single immature (~ 1-year-old) male double-haploid fish and frozen in liquid nitrogen and stored at -80C until total RNA isolation. Total RNA was isolated using TRIzolâ„¢ (Invitrogen, Carlsbad, CA) from fourteen tissues; white muscle, red muscle, testis, spleen, kidney, head kidney, pituitary, stomach, brain, heart, intestine, gill, skin, liver. Equal masses of total RNAs from various tissues were pooled and used to construct the 454 library.@�� Trout transcriptome-454SRP001007Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesOtherBackground: Rainbow trout is important fish species for aquaculture and biomedical research but has no genomic data. Until genome sequence becomes available, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Large-scale EST (258,973) Singer sequences are publicly available for rainbow trout. However, the nature of duplicated rainbow trout genome hinders assembly and annotation of the EST sequences. Additionally, previous efforts aimed at SNP discovery for rainbow trout using ESTs were unsuccessful, mainly, due to difficulties parsing allelic variation from the high frequency of duplicated genes. Results: High-throughput shotgun deep sequencing of the rainbow trout double-haploid transcriptome using DNA 454-pyrosequencing technology has been successfully applied yielding about 1.3 million reads with an average length of 344bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus sequences (TCs) (Average length 662 nt) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing Singer sequences resulted in 161,818 TCs (Average length 758 nt) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed similarity to the expected transcriptome of other fish species with known genome sequences, suggesting a genome-wide representation of the rainbow trout transcriptome sequence. Conclusion: The 454 library added great amount of new EST sequences and identified new genes. In addition, it improved assembly and annotation of the rainbow trout Sanger EST. The 454 library is a new tool for functional genome research in rainbow trout. It provides a reference sequence to identify gene duplications, allelic variations; distinguish true/false SNPs as well as for digital gene expression and proteomic research in rainbow trout.Oncorhynchus mykissA�d SRA009276West Virginia University,Animal Biotechnology and Genomics2009-08-052018-05-10 18:11:11
c c �ۂS O ! �5 �Q �Y) �I! E E �] ; �Q�3 ?O!3A0�X Rainbow trout transcriptome-454-2SRR0207402013-07-26A$N A�X�v A0%� Rainbow trout transcriptome analysis using Sanger and 454-Pyrosequencing approachesSRX007396Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesMessenger RNA was isolated from total RNA using the Oligotex mRNA Mini kit (Qiagen, CA). First and second strand cDNA were synthesized from 200ng of mRNA using the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen, CA) with 100 µM random hexamer primers (Fermentas, USA). Double-stranded cDNA was cleaned up with a QIAquick Minelute PCR purification column (Qiagen, CA). Double-stranded DNA was nebulized with the nebulization kit supplied with the GS Titanium Library Preparation kit (Roche/454 Life Sciences, CT) following their recommendations (30psi for 1 minute) and cleaned up with a QIAquick PCR minelute column and eluted in 50ul EB. Nebulized cDNA was blunt-ended (25 µl water, 10 µl 10x T4 DNA Ligase buffer (NEB), 4 µl 10 mM dNTP mix, 5 µl T4 DNA polymerase (3 U/µl) (NEB), 1 µl Klenow polymerase (5 U/ µl) (NEB), and 5 µl Polynucleotide kinase (10 U/µl) (NEB) and cleaned up with a Qiaquick PCR minelute column and eluted in 32ul EB. A dA-overhang was added at 3’ end of cDNA by adding the following to the blunt-ended cDNA: 5 µl 10x buffer 2 (NEB), 10 µl 1 mM dATP and 3 µl Klenow exo-minus polymerase (5 U/µl) (NEB). The reaction was incubated at 370C for 30 minutes and then cleaned up with a QIAquick MiniElute column and eluted in 10 µl EB. The cDNA was adaptored with Titanium adaptors (Roche/454 Life Sciences, CT) by adding 9 µl water, 25 µl 2x Rapid Ligase buffer (Enzymatics, MA) 5 µl (50 µM) Titanium adapter A/B mix and 1 µl T4 DNA Ligase (600 U/µl (Enzymatics, MA) and incubated the ligation reaction at room temperature for 15 minutes. The reaction was cleaned up using a Qiaquick MiniElute column (Qiagen), eluting the cDNA in 20 µl EB. Adaptored cDNA was run on a E-GEL EX 2% agarose (Invitrogen, CA) following the manufacturer instructions and cDNAs in the size range of 400-800bp were excised from the gel and purified with a Qiagen’s Gel Extraction kit and the cDNA was eluted in 30 µl EB. One µl of the gel- purified cDNA was used as template for amplification in 50 µl PCR reactions containing 10 µl 5x Phusion Buffer HF (NEB), 25 µM Adapter A_For p j rimer (5’CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGT3’), 25 µM Adapter B_For primer (5’CCTATCCCCTGTGTGCCTTGGCAGTCTCAGT3’), 3% DMSO, 10 mM dNTPs and 1 U Phusion polymerase (Finnzymes/NEB, USA). The PCR conditions were as follows: 980C for 30 seconds, followed by 15 cycles with 980C for 10 seconds, 680C for 30 seconds and 720C for 30 seconds, with a final extension of 720C for 5 minute and cleaned up with a Qiaquick minelute PCR column. Normalization of cDNA library The cDNA library was normalized according to the protocol described in the Trimmer Direct Kit (Evrogen, Russia). In brief, 300 ng of cDNA were incubated at 950C for 5 minutes followed by incubation at 680C for 4 hours in the hybridization buffer included in the kit (50 mM Hepes, pH7.5 and 0.5 M NaCl). After the incubation, the reaction was treated with ¼ units of duplex specific nuclease (DSN). The normalized cDNA was then amplified from 1 µl of DSN-treated cDNA by PCR reactions (10 cycles) described above and gel purified for the fragment size of 400-800 bp as described above.454ESTTRANSCRIPTOMICcDNASINGLE - READ_INDEX: 0; READ_CLASS: Technical Read; READ_TYPE: Adapter; BASE_COORD: 1 || READ_INDEX: 1; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 5LS454454 GS FLXINSTRUMENT_MODEL: 454 GS FLXA'�� double-haploid rainbow troutSRS004650 VTissues were collected from a single immature (~ 1-year-old) male double-haploid fish and frozen in liquid nitrogen and stored at -80C until total RNA isolation. Total RNA was isolated using TRIzolâ„¢ (Invitrogen, Carlsbad, CA) from fourteen tissues; white muscle, red muscle, testis, spleen, kidney, head kidney, pituitary, stomach, brain, heart, intestine, gill, skin, liver. Equal masses of total RNAs from various tissues were pooled and used to construct the 454 library.@�� Trout transcriptome-454SRP001007Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesOtherBackground: Rainbow trout is important fish species for aquaculture and biomedical research but has no genomic data. Until genome sequence becomes available, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Large-scale EST (258,973) Singer sequences are publicly available for rainbow trout. However, the nature of duplicated rainbow trout genome hinders assembly and annotation of the EST sequences. Additionally, previous efforts aimed at SNP discovery for rainbow trout using ESTs were unsuccessful, mainly, due to difficulties parsing allelic variation from the high frequency of duplicated genes. Results: High-throughput shotgun deep sequencing of the rainbow trout double-haploid transcriptome using DNA 454-pyrosequencing technology has been successfully applied yielding about 1.3 million reads with an average length of 344bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus sequences (TCs) (Average length 662 nt) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing Singer sequences resulted in 161,818 TCs (Average length 758 nt) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed similarity to the expected transcriptome of other fish species with known genome sequences, suggesting a genome-wide representation of the rainbow trout transcriptome sequence. Conclusion: The 454 library added great amount of new EST sequences and identified new genes. In addition, it improved assembly and annotation of the rainbow trout Sanger EST. The 454 library is a new tool for functional genome research in rainbow trout. It provides a reference sequence to identify gene duplications, allelic variations; distinguish true/false SNPs as well as for digital gene expression and proteomic research in rainbow trout.Oncorhynchus mykissA�d SRA009276West Virginia University,Animal Biotechnology and Genomics2009-08-052018-05-10 18:11:11
c �G���O U! ! !K ? ) 3 W ! �-# e�W �o 3AK�� 14710B-3_L8_I20010.R1.clean.fastq.gzSRR59646222017-08-24Ad��� A�ah AH�� 14710B-3SRX3122356RNA-seq for MCF-7 breast cancerβ-estradiol_treat114710B-3RNA-SeqTRANSCRIPTOMICPCRPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AF
W 14710B-3SRS2456862%�isolate: treat1 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human@��� PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism.A&�� SRA602313National Research Institute for Health and Family PlanningNational Research Institute for Health and Family2018-05-10 18:11:11�ۂS O ! �5 �Q �Y) �I! E E �] ; �Q�3 ?O!3A0�W Rainbow trout transcriptome-454-1SRR0207392013-07-26A#�p A��! A0%� Rainbow trout transcriptome analysis using Sanger and 454-Pyrosequencing approachesSRX007396Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approachesMessenger RNA was isolated from total RNA using the Oligotex mRNA Mini kit (Qiagen, CA). First and second strand cDNA were synthesized from 200ng of mRNA using the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen, CA) with 100 µM random hexamer primers (Fermentas, USA). Double-stranded cDNA was cleaned up with a QIAquick Minelute PCR purification column (Qiagen, CA). Double-stranded DNA was nebulized with the nebulization kit supplied with the GS Titanium Library Preparation kit (Roche/454 Life Sciences, CT) following their recommendations (30psi for 1 minute) and cleaned up with a QIAquick PCR minelute column and eluted in 50ul EB. Nebulized cDNA was blunt-ended (25 µl water, 10 µl 10x T4 DNA Ligase buffer (NEB), 4 µl 10 mM dNTP mix, 5 µl T4 DNA polymerase (3 U/µl) (NEB), 1 µl Klenow polymerase (5 U/ µl) (NEB), and 5 µl Polynucleotide kinase (10 U/µl) (NEB) and cleaned up with a Qiaquick PCR minelute column and eluted in 32ul EB. A dA-overhang was added at 3’ end of cDNA by adding the following to the blunt-ended cDNA: 5 µl 10x buffer 2 (NEB), 10 µl 1 mM dATP and 3 µl Klenow exo-minus polymerase (5 U/µl) (NEB). The reaction was incubated at 370C for 30 minutes and then cleaned up with a QIAquick MiniElute column and eluted in 10 µl EB. The cDNA was adaptored with Titanium adaptors (Roche/454 Life Sciences, CT) by adding 9 µl water, 25 µl 2x Rapid Ligase buffer (Enzymatics, MA) 5 µl (50 µM) Titanium adapter A/B mix and 1 µl T4 DNA Ligase (600 U/µl (Enzymatics, MA) and incubated the ligation reaction at room temperature for 15 minutes. The reaction was cleaned up using a Qiaquick MiniElute column (Qiagen), eluting the cDNA in 20 µl EB. Adaptored cDNA was run on a E-GEL EX 2% agarose (Invitrogen, CA) following the manufacturer instructions and cDNAs in the size range of 400-800bp were excised from the gel and purified with a Qiagen’s Gel Extraction kit and the cDNA was eluted in 30 µl EB. One µl of the gel- purified cDNA was used as template for amplification in 50 µl PCR reactions containing 10 µl 5x Phusion Buffer HF (NEB), 25 µM Adapter A_For p l
C � u7 C �n���HP -! ! !Y �) 3 W ! �# � �! ;_ 3AL � RNA5_R2.fastq.gzSRR59975332017-09-01Aqv� A�?� AH�� RNA5SRX3153039RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA5RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA5SRS2484893
ѯisolate: 770444.001 || cultivar: Camansi || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�8���O U! ! !K ) 3 W ! �1# e�W �o 3AK��� 14710B-2_L8_I20009.R2.clean.fastq.gzSRR59646232017-08-24AcO- A�+�� AH��� 14710B-2SRX3122355RNA-seq for MCF-7 breast cancercontrol214710B-2RNA-SeqTRANSCRIPTOMICPCRPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AF
V� 14710B-2SRS2456861%�isolate: control2 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human@��� PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism.A&�� SRA602313National Research Institute for Health and Family PlanningNational Research Institute for Health and Family2018-05-10 18:11:11�G���O U! ! !K ? ) 3 W ! �-# e�W �o 3AK��� 14710B-4_L8_I20011.R1.clean.fastq.gzSRR59646212017-08-24Ah�M� A�l� AH��� 14710B-4SRX3122357RNA-seq for MCF-7 breast cancerβ-estradiol_treat214710B-4RNA-SeqTRANSCRIPTOMICPCRPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AF
X 14710B-4SRS2456864%�isolate: treat2 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human@��� PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism.A&�� SRA602313National Research Institute for Health and Family PlanningNational Research Institute for Health and Family2018-05-10 18:11:11�8��� O U! ! !K ) 3 W ! �1# e�W �o 3AK�� 14710B-1_L8_I20008.R2.clean.fastq.gzSRR59646242017-08-24Ael.� A༄� AH�� 14710B-1SRX3122354RNA-seq for MCF-7 breast cancercontrol114710B-1RNA-SeqTRANSCRIPTOMICPCRPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AF
W� 14710B-1SRS2456863%�isolate: control1 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human@��� PRJNA399772SRP116052Role of ß-estradiol in breast cancer.OtherThis study aimed to investigate the role of ß-estradiol in MCF-7 breast cancer (BC) mechanism.A&�� SRA602313National Research Institute for Health and Family PlanningNational Research Institute for Health and Family2018-05-10 18:11:11
�k���JP /! ! !Q �) 3 W ! �# � �! ;_ 3AL �� RNA24_R2.fastq.gzSRR59975242017-09-01Ar��� A�R AH�� RNA24SRX3153048RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA24RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA24SRS2484902��isolate: 900261.001 || cultivar: Samoan 2 || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�s���IP /! ! !Y �) 3 W ! � # � �! ;_ 3AL �� RNA34_R2.fastq.gzSRR59975322017-09-01Ax� @ A�je� AH�� RNA34SRX3153040RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA34RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA34SRS2484894
ѯisolate: 890455.001 || cultivar: Ulu fatu || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
� �n���LP /! ! !Y �) 3 W ! �# � �! ;_ 3AL �� RNA35_R1.fastq.gzSRR59975282017-09-01Ap�@ A�Dz AH�� RNA35SRX3153044RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA35RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA35SRS2484898
ѯisolate: 389.001 || cultivar: Kapiak || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11����KQ /! ! !� �) 3 W ! �# � �! ;_ 3AL � RNA48_R1.fastq.gzSRR59975272017-09-01Ae6�� A�a� AH�� RNA48SRX3153045RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA48RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA48SRS2484899Z�isolate: 890184.001 || cultivar: Luthar || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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� ����NQ /! ! !� �) 3 W ! �# � �! ;_ 3AL � RNA10_R2.fastq.gzSRR59975232017-09-01Aql� A��;l� AH�� RNA10SRX3153049RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA10RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA10SRS2484903Z�isolate: 790490.001 || cultivar: Rotuma || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�r���MP /! ! !Y �) 3 W ! �# � �! ;_ 3AL �� RNA37_R2.fastq.gzSRR59975342017-09-01A�P�` A���π AH�� RNA37SRX3153038RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA37RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA37SRS2484892
ѯisolate: 980212.001 || cultivar: Camansi || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
� �� �q���PP /! ! !Y �) 3 W ! �# � �! ;_ 3AL � RNA21_R2.fastq.gzSRR59975252017-09-01Av�!� A� ��� AH�� RNA21SRX3153047RNA-Seq of Artocarpus altilis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA21RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA21SRS2484901��isolate: 900265.001 || cultivar: Karawa || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�
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. A�~e@ AH��� RNA17SRX3153054RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA17RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA17SRS2484908Z�isolate: 790487.001 || cultivar: Unk (Huehue) || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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% �f���RP +! ! !Y �) 3 W ! �# � �! ;_ 3AL �� EW2_R2.fastq.gzSRR59975302017-09-01Au��p A�WP` AH�� EW2SRX3153042RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingEW2RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� EW2SRS2484896
ѯisolate: 501.005 || cultivar: Kapiak || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�i���QP /! ! !Q �) 3 W ! �# � �! ;_ 3AL � RNA49_R2.fastq.gzSRR59975392017-09-01Am��� A�W[B@ AH�� RNA49SRX3153033RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA49RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA49SRS2484887��isolate: 910265.001 || cultivar: Rotuma || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
� �j���TP /! ! !Q �) 3 W ! �# � �! ;_ 3AL �� RNA26_R2.fastq.gzSRR59975162017-09-01AoW� A�Y AH��� RNA26SRX3153056RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA26RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFQ � RNA26SRS2484910��isolate: 890167.002 || cultivar: Meisaip || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�|���SP +! ! !q �) 3 W ! �'# � �! ;_ 3AL � EW4_R1.fastq.gzSRR59975292017-09-01A���P B�@+ AH�� EW4SRX3153043RNA-Seq of Artocarpus camansi root, stem, and leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingEW4RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� EW4SRS2484897
ѯisolate: 501 || cultivar: Kapiak || dev_stage: Seedling || geo_loc_name: USA: Hawaii || tissue: Root, Stem, and Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
�n���VP -! ! !Y �) 3 W ! �# � �! ;_ 3AL � RNA2_R1.fastq.gzSRR59975352017-09-01Al�]� A�3�� AH�� RNA2SRX3153037RNA-Seq of Artocarpus camansi perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA2RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA2SRS2484891
ѯisolate: 910280.001 || cultivar: Meikole || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�h���UP +! ! !Y �) 3 W ! �# � �! ;_ 3AL � EW3_R2.fastq.gzSRR59975372017-09-01Awx� A�:@ AH�� EW3SRX3153035RNA-Seq of Artocarpus altilis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingEW3RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� EW3SRS2484889��isolate: 30042.001 || cultivar: Toneno || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
�i���XP /! ! !Q �) 3 W ! �# � �! ;_ 3AL � RNA25_R1.fastq.gzSRR59975172017-09-01Ap\�0 A��~� AH�� RNA25SRX3153055RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA25RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFQ RNA25SRS2484909��isolate: 890479.002 || cultivar: Meisei || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�r���WP -! ! !c �) 3 W ! �# � �! ;_ 3AL � RNA7_R1.fastq.gzSRR59975312017-09-01AkR� A厺� AH�� RNA7SRX3153041RNA-Seq of Artocarpus mariannensis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA7RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA7SRS2484895
Ѽisolate: 900252.002 || cultivar: Dugdug || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
����ZQ /! ! !� �) 3 W ! �# � �! ;_ 3AL � RNA40_R1.fastq.gzSRR59975192017-09-01AYڮ@ A�f�~� AH�� RNA40SRX3153053RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA40RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA40SRS2484907Z�isolate: 910269.001 || cultivar: Faine || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�f���YP /! ! !Q �) 3 W ! � # � �! ;_ 3AL �� RNA38_R1.fastq.gzSRR59975362017-09-01AvF\0 A� AH�� RNA38SRX3153036RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA38RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA38SRS2484890��isolate: 880690.001 || cultivar: Kea || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
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�) 3 W ! �'# � �! ;_ 3AL �� RNA36_R2.fastq.gzSRR59975202017-09-01A`�` A��k�� AH�� RNA36SRX3153052RNA-Seq of Artocarpus altilis x Artocarpus mariannensis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA36RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA36SRS2484906Z�isolate: 890173.002 || cultivar: Ulu afa elise || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�
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�) 3 W ! �# � �! ;_ 3AL � RNA32_R1.fastq.gzSRR59975212017-09-01Arb�� A�~!� AH�� RNA32SRX3153051RNA-Seq of Artocarpus altilis x Artocarpus mariannensis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA32RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP� RNA32SRS2484905Z�isolate: 890174.001 || cultivar: Ulu afa || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
����^Q /! ! !� �) 3 W ! �# � �! ;_ 3AL �� RNA16_R2.fastq.gzSRR59975262017-09-01Av`70 A��� AH�� RNA16SRX3153046RNA-Seq of Artocarpus altilis x Artocarpus mariannensis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA16RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA16SRS2484900Z�isolate: 890183.001 || cultivar: Midolab || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11�i���]P /! ! !Q �) 3 W ! �# � �! ;_ 3AL �� RNA39_R1.fastq.gzSRR59975382017-09-01As�� A�P�r AH�� RNA39SRX3153034RNA-Seq of Artocarpus altilis leafRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingRNA39RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� RNA39SRS2484888��isolate: 790485.001 || cultivar: Puupuu || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
}
} ����rP q! ! !+ �{- # G ! �q# �1;�7% ? 3AL �� CCGTCC_X_1_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975602017-09-01A��@ A���E� AH� D3SRX3153086diploid tumor 3DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D3WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ
D3SRS2484936%�isolate: breast cancer patient from Sweden || age: 45 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11�g���_P +! ! !Y �) 3 W ! �# � �! ;_ 3AL �� EW1_R2.fastq.gzSRR59975222017-09-01Au4�� A�w� AH�� EW1SRX3153050RNA-Seq of Artocarpus altilis perianthRibo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencingEW1RNA-SeqTRANSCRIPTOMICcDNAPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AFP�� EW1SRS2484904��isolate: 970236 || cultivar: Ulu fiti || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant@�� PRJNA311339SRP116664Transcriptome analysis of domesticated breadfruit and its wild relativesOtherThe goal of this research was to provide a better understanding of the genomic effects of the domestication process in breadfruit and, ultimately, to develop genomic resources that may facilitate the development of improved cultivars in the future. A reference transcriptome of breadfruit was assembled de novo and characterized. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that have potentially resulted from domestication or natural selection. Focus was placed on analyzing MADS-box genes, which often regulate plant development, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.ArtocarpusA&�0 SRA604752Northwestern UniversityProgram in Plant Biology and Conservation2018-05-10 18:11:11
c c ����sP {! ! !/ �{- # G ! �q# �1;�7% ? 3AL � GTTTCG_1_3_000000000-ADYRF.750_BUSTARD-2015-06-23.fq.gzSRR59975692017-09-01A~m� A�N�5` AH� � A5SRX3153077aneuploid tumor 5DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A5WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ� A5SRS2484927%�isolate: breast cancer patient from Sweden || age: 64 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
j j ����tP q! ! !+ �{- # G ! �q# �1;�7% ? 3AL ACTGAT_X_1_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975662017-09-01AZV_@ A̛�@ AH� D5SRX3153080diploid tumor 5DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D5WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ
D5SRS2484930%�isolate: breast cancer patient from Sweden || age: 69 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
c c ����uP {! ! !/ �{- # G ! �q# �1;�7% ? 3AL � GTGGCC_1_3_000000000-ADYRF.750_BUSTARD-2015-06-23.fq.gzSRR59975672017-09-01Auٸ A��� AH�� A1SRX3153079aneuploid tumor 1DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A1WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ � A1SRS2484929%�isolate: breast cancer patient from Sweden || age: 40 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
S S �'���vP {! ! !/ �{- # G ! �# �1;�7% ? 3AL � ATGTCA_1_1_000000000-ADYRF.750_BUSTARD-2015-06-23.fq.gzSRR59975652017-09-01AvW� A�7�^` AH�� A3SRX3153081aneuploid tumor 3DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A3WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ
� A3SRS2484931%�isolate: breast cancer patient from Sweden || age: 53 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
j j ����wP q! ! !+ �{- # G ! �q# �1;�7% ? 3AL � GAGTGG_X_3_AH3KYTAFXX.811_NEXTSEQ-2015-09-04.fq.gzSRR59975612017-09-01Aj�a@ A݊c1 AH�� D4SRX3153085diploid tumor 4DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D4WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ � D4SRS2484935%�isolate: breast cancer patient from Sweden || age: 62 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
X X �"���xP q! ! !/ �{- # G ! �# �1;�7% ? 3AL �� GTCCGC_X_3_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975642017-09-01A[> A� A� AH� A2SRX3153082aneuploid tumor 2DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A2WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ A2SRS2484932%�isolate: breast cancer patient from Sweden || age: 60 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
V V �$���yP q! ! !+ �{- # G ! �# �1;�7% ? 3AL � ATTCCT_X_1_AH3KYTAFXX.811_NEXTSEQ-2015-09-04.fq.gzSRR59975632017-09-01A�(� A�A�P AH�� D2SRX3153083diploid tumor 2DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D2WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ D2SRS2484934%�isolate: breast cancer patient from Sweden || age: 72 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead not by breast cancer || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
X X �"���zP q! ! !/ �{- # G ! �# �1;�7% ? 3AL Ā ATCACG_X_3_AH3KYTAFXX.811_NEXTSEQ-2015-09-04.fq.gzSRR59975702017-09-01AX,�� Aʇ�� AH� A6SRX3153076aneuploid tumor 6DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A6WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ A6SRS2484926%�isolate: breast cancer patient from Sweden || age: 46 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
j j ����{P q! ! !+ �{- # G ! �q# �1;�7% ? 3AL �� TTAGGC_X_1_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975622017-09-01AtL�P A��` AH� D1SRX3153084diploid tumor 1DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.D1WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ � D1SRS2484933%�isolate: breast cancer patient from Sweden || age: 66 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Alive || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
� X � �_���7Q '! ! ! !!� ) �7 3 W !! �g �?9�# A 3AM/� GSM2791401_r1SRR60677392017-10-11A��t� A�B8@ GSM2791401AI� GSM2791401SRX3209941GSM2791401: HBCx-22 PDX treated with vehicle #3; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500AF�� GSM2791401SRS2534923%�source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positive@��� GSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177A'?4 SRA612572submission brokered by GEOGEO2018-05-10 18:11:11�"���|P q! ! !/ �{- # G ! �# �1;�7% ? 3AL À GTGAAA_X_1_AH3KY7AFXX.816_NEXTSEQ-2015-09-15.fq.gzSRR59975682017-09-01AlA� A�
�@ AH� A4SRX3153078aneuploid tumor 4DNA was extracted from a representative area of a 50 ?m section using proteinase K digestion. Targeted next generation sequencing was performed with a capture assay, termed OncoVar, which was designed to sequence coding exons of 563 cancer related genes (Boikos SA et al. JAMA Oncol 2016). The resulting paired-end libraries were sequenced on Illumina NextSeq 500 sequencers.A4WXSGENOMICHybrid SelectionPAIRED - ILLUMINANextSeq 500INSTRUMENT_MODEL: NextSeq 500AFQ A4SRS2484928%�isolate: breast cancer patient from Sweden || age: 49 || biomaterial_provider: Gert Auer Department of Oncology-Pathology, arolinska Universitetssjukhuset Solna, 171 76 Stockholm, Sweden || sex: female || tissue: breast cancer tumor || disease: breast cancer || health_state: Dead by breast cancer || BioSampleModel: Human@�� PRJNA399503SRP116668Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patientsWhole Genome SequencingWe analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors. We analyzed five diploid and six aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however TP53 mutations wer not observed in diploid tumors, but were observed in all aneuploid tumors.Homo sapiensA&�6 SRA604756National Cancer InstituteGenetics2018-05-10 18:11:11
8 �8 �]���9Q '! ! ! !!� ) �7 3 W !! �e �?9�# A 3AM1 GSM2791404_r1SRR60677422017-10-11A�`W� A�I�t GSM2791404AI�� GSM2791404SRX3209944GSM2791404: HBCx-22 PDX treated with RAD140 #6; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500AF� GSM2791404SRS2534926%�source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positive@��� GSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177A'?4 SRA612572submission brokered by GEOGEO2018-05-10 18:11:11�_���8Q '! ! ! !!� ) �7 3 W !! �g �?9�# A 3AM/ GSM2791400_r1SRR60677382017-10-11A��7� A��t GSM2791400AI� GSM2791400SRX3209940GSM2791400: HBCx-22 PDX treated with vehicle #2; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500AF� GSM2791400SRS2534922%�source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positive@��� GSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177A'?4 SRA612572submission brokered by GEOGEO2018-05-10 18:11:11
8 �8 �]���;Q '! ! ! !!� ) �7 3 W !! �e �?9�# A 3AM0 GSM2791402_r1SRR60677402017-10-11A� a( A찚� GSM2791402AI� � GSM2791402SRX3209942GSM2791402: HBCx-22 PDX treated with RAD140 #4; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500AF�� GSM2791402SRS2534925%�source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positive@��� GSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177A'?4 SRA612572submission brokered by GEOGEO2018-05-10 18:11:11�_���:Q '! ! ! !!� ) �7 3 W !! �g �?9�# A 3AM.� GSM2791399_r1SRR60677372017-10-11A��dX A�d��@ GSM2791399AI� GSM2791399SRX3209939GSM2791399: HBCx-22 PDX treated with vehicle #1; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500AF�� GSM2791399SRS2534921%�source_name: HBCx-22 PDX treated with vehicle || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positive@��� GSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177A'?4 SRA612572submission brokered by GEOGEO2018-05-10 18:11:11
� � �]���<Q '! ! ! !!� ) �7 3 W !! �e �?9�# A 3AM0� GSM2791403_r1SRR60677412017-10-11A�'A� A��#@ GSM2791403AI� GSM2791403SRX3209943GSM2791403: HBCx-22 PDX treated with RAD140 #5; Homo sapiens; RNA-SeqGSE104177RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Total RNA from xenograft samples and cells was extracted using the RNeasy Mini Kit (Qiagen), with a DNase incubation step included to ensure complete removal of genomic DNA. Purified RNA samples were converted into cDNA libraries using the TrueSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA). Libraries were quantified, normalized, and pooled before being subjected to HiSeq 2×50bp paired end sequencing on an Illumina sequencing platform.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500AF� GSM2791403SRS2534924%�source_name: HBCx-22 PDX treated with RAD140 || xenograft host: female athymic nude mice (Foxn1nu) || tissue: breast cancer patient-derived xenografts (PDX) || tissue type: snapfrozen xenograft specimen || tag: Hormone receptor positive@��� GSE104177SRP118776Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenograftsTranscriptome AnalysisThese data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression. Overall design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the studyGSE104177A'?4 SRA612572submission brokered by GEOGEO2018-05-10 18:11:11
� � �4���yP '! ! ! !!g ) �{ 3 W ?!! �= �K9�) A 3AM3� GSM2791564_r1SRR60688782017-10-11A�l� A��-v� GSM2791564AI� GSM2791564SRX3210847GSM2791564: 37NormPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791564AF� GSM2791564SRS2535694%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O101 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �;���zP '! ! ! !!i ) �{ 3 W ?!! �I �K9�) A 3AM>� GSM2791586_r1SRR60689002017-10-11A���� A�5j*� GSM2791586AI� GSM2791586SRX3210869GSM2791586: 83NPP_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791586AF� GSM2791586SRS2535716%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: U784 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �=���{P '! ! ! !!g ) �{ 3 W ?!! �O �K9�) A 3AM= GSM2791583_r1SRR60688972017-10-11A��� A��� GSM2791583AI�
� GSM2791583SRX3210866GSM2791583: 68HPP_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791583AF�� GSM2791583SRS2535713%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: U781 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �;���|P '! ! ! !!i ) �{ 3 W ?!! �I �K9�) A 3AM:� GSM2791578_r1SRR60688922017-10-11A��� A��� GSM2791578AI� GSM2791578SRX3210861GSM2791578: 67NPP_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791578AF� GSM2791578SRS2535708%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: U776 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �/���}P '! ! ! !!g ) �{ 3 W ?!! �3 �K9�) A 3AM2 GSM2791561_r1SRR60688752017-10-11A�z�X A����� GSM2791561AI�� GSM2791561SRX3210844GSM2791561: 38HipTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791561AF�� GSM2791561SRS2535691%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Total mRNA || barcode: O098 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �:���~P '! ! ! !!i ) �{ 3 W ?!! �G �K9�) A 3AM9 GSM2791575_r1SRR60688892017-10-11A��x A���.� GSM2791575AI� � GSM2791575SRX3210858GSM2791575: 44HipPPPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791575AF�� GSM2791575SRS2535705%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: O112 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �9���P '! ! ! !!m ) �{ 3 W ?!! �A �K9�) A 3AM6� GSM2791570_r1SRR60688842017-10-11A�!x@ A�'�� GSM2791570AI� GSM2791570SRX3210853GSM2791570: 43NormPPTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791570AF� � GSM2791570SRS2535699%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: O107 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �9��� P '! ! ! !!m ) �{ 3 W ?!! �A �K9�) A 3AM2� GSM2791562_r1SRR60688762017-10-11A��� A�<� GSM2791562AI� GSM2791562SRX3210845GSM2791562: 39NormPPTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791562AF� GSM2791562SRS2535692%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: O099 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �>���P '! ! ! !!g ) �{ 3 W ?!! �Q �K9�) A 3AM<� GSM2791582_r1SRR60688962017-10-11A�p�x A��� GSM2791582AI�
GSM2791582SRX3210865GSM2791582: 67NPP_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791582AF� GSM2791582SRS2535712%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: U780 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �:���P '! ! ! !!i ) �{ 3 W ?!! �G �K9�) A 3AM; GSM2791579_r1SRR60688932017-10-11A���p A�6U GSM2791579AI� � GSM2791579SRX3210862GSM2791579: 68HPP_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791579AF�� GSM2791579SRS2535709%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: U777 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �3���P '! ! ! !!e ) �{ 3 W ?!! �= �K9�) A 3AM=� GSM2791584_r1SRR60688982017-10-11As�� A�5S GSM2791584AI� GSM2791584SRX3210867GSM2791584: 81N_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791584AF� GSM2791584SRS2535714%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Total mRNA || barcode: U782 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �2���P '! ! ! !!e ) �{ 3 W ?!! �; �K9�) A 3AM> GSM2791585_r1SRR60688992017-10-11Az��� A�öM GSM2791585AI�� GSM2791585SRX3210868GSM2791585: 82H_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791585AF�� GSM2791585SRS2535715%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Total mRNA || barcode: U783 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �<���P '! ! ! !!k ) �{ 3 W ?!! �I �K9�) A 3AM4� GSM2791566_r1SRR60688802017-10-11A�x�� A� �� GSM2791566AI� GSM2791566SRX3210849GSM2791566: 39NormPPPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791566AF�
GSM2791566SRS2535696%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: O103 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �2���P '! ! ! !!e ) �{ 3 W ?!! �; �K9�) A 3AM4 GSM2791565_r1SRR60688792017-10-11A(� A�@@ GSM2791565AI�� GSM2791565SRX3210848GSM2791565: 38HipPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791565AF� � GSM2791565SRS2535695%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: O102 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �2���P '! ! ! !!e ) �{ 3 W ?!! �; �K9�) A 3AM: GSM2791577_r1SRR60688912017-10-11A�T%� A��� GSM2791577AI�
� GSM2791577SRX3210860GSM2791577: 66H_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791577AF�� GSM2791577SRS2535707%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Total mRNA || barcode: U775 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �3���P '! ! ! !!e ) �{ 3 W ?!! �= �K9�) A 3AM9� GSM2791576_r1SRR60688902017-10-11A}h� A�v� GSM2791576AI�
GSM2791576SRX3210859GSM2791576: 65N_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791576AF� GSM2791576SRS2535706%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Total mRNA || barcode: U774 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �6��� P '! ! ! !!c ) �{ 3 W ?!! �E �K9�) A 3AM;� GSM2791580_r1SRR60688942017-10-11Ay�� A�u)! GSM2791580AI� GSM2791580SRX3210863GSM2791580: 65N_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791580AF� GSM2791580SRS2535710%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Polysomal mRNA || barcode: U778 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
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P '! ! ! !!i ) �{ 3 W ?!! �5 �K9�) A 3AM1� GSM2791560_r1SRR60688742017-10-11A��$ A���܀ GSM2791560AI� GSM2791560SRX3210843GSM2791560: 37NormTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791560AF� GSM2791560SRS2535690%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Total mRNA || barcode: O097 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �/��� P '! ! ! !!g ) �{ 3 W ?!! �3 �K9�) A 3AM6 GSM2791569_r1SRR60688832017-10-11A� A�/'� GSM2791569AI�� GSM2791569SRX3210852GSM2791569: 42HipTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791569AF� GSM2791569SRS2535700%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Total mRNA || barcode: O106 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �2��� P '! ! ! !!e ) �{ 3 W ?!! �; �K9�) A 3AM8 GSM2791573_r1SRR60688872017-10-11A��( A���� GSM2791573AI�� GSM2791573SRX3210856GSM2791573: 42HipPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791573AF�
� GSM2791573SRS2535703%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: O110 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
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P '! ! ! !!i ) �{ 3 W ?!! �5 �K9�) A 3AM5� GSM2791568_r1SRR60688822017-10-11A���H A���Հ GSM2791568AI� GSM2791568SRX3210851GSM2791568: 41NormTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791568AF�
� GSM2791568SRS2535697%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Total mRNA || barcode: O105 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �4���P '! ! ! !!g ) �{ 3 W ?!! �= �K9�) A 3AM7� GSM2791572_r1SRR60688862017-10-11A�7� A���v� GSM2791572AI� GSM2791572SRX3210855GSM2791572: 41NormPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791572AF�
GSM2791572SRS2535702%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O109 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �:���P '! ! ! !!i ) �{ 3 W ?!! �G �K9�) A 3AM5 GSM2791567_r1SRR60688812017-10-11A�k� A�0� GSM2791567AI�� GSM2791567SRX3210850GSM2791567: 40HipPPPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791567AF� GSM2791567SRS2535698%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: O104 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �5���P '! ! ! !!c ) �{ 3 W ?!! �C �K9�) A 3AM@ GSM2791589_r1SRR60689032017-10-11A��%( A��� � GSM2791589AI�� GSM2791589SRX3210872GSM2791589: 82H_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791589AF�� GSM2791589SRS2535719%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: U787 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �5���P '! ! ! !!c ) �{ 3 W ?!! �C �K9�) A 3AM< GSM2791581_r1SRR60688952017-10-11A~f� A� �Q� GSM2791581AI� � GSM2791581SRX3210864GSM2791581: 66H_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791581AF�� GSM2791581SRS2535711%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: U779 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �6���P '! ! ! !!c ) �{ 3 W ?!! �E �K9�) A 3AM?� GSM2791588_r1SRR60689022017-10-11A��( A�EO� GSM2791588AI� GSM2791588SRX3210871GSM2791588: 81N_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791588AF� GSM2791588SRS2535718%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Polysomal mRNA || barcode: U786 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �7���P '! ! ! !!k ) �{ 3 W ?!! �? �K9�) A 3AM7 GSM2791571_r1SRR60688852017-10-11A��� A�h�! GSM2791571AI�� GSM2791571SRX3210854GSM2791571: 44HipPPTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791571AF� � GSM2791571SRS2535701%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: O108 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �=���P '! ! ! !!g ) �{ 3 W ?!! �O �K9�) A 3AMA GSM2791591_r1SRR60689052017-10-11A��� A��Y� GSM2791591AI�� GSM2791591SRX3210874GSM2791591: 84HPP_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791591AF�� GSM2791591SRS2535721%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: U789 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �7���P '! ! ! !!k ) �{ 3 W ?!! �? �K9�) A 3AM3 GSM2791563_r1SRR60688772017-10-11A�2�@ A�l� GSM2791563AI�� GSM2791563SRX3210846GSM2791563: 40HipPPTotal; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791563AF�� GSM2791563SRS2535693%�source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: O100 || replicate: Biological replicate 1@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �:���P '! ! ! !!i ) �{ 3 W ?!! �G �K9�) A 3AM? GSM2791587_r1SRR60689012017-10-11A��� A� GSM2791587AI�� GSM2791587SRX3210870GSM2791587: 84HPP_Total; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791587AF�� GSM2791587SRS2535717%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: U785 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �>���P '! ! ! !!g ) �{ 3 W ?!! �Q �K9�) A 3AM@� GSM2791590_r1SRR60689042017-10-11A��8 A��≀ GSM2791590AI� GSM2791590SRX3210873GSM2791590: 83NPP_Poly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeqâ„¢ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791590AF� GSM2791590SRS2535720%�source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: U788 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� � �<���P '! ! ! !!k ) �{ 3 W ?!! �I �K9�) A 3AM8� GSM2791574_r1SRR60688882017-10-11A��� A��y! GSM2791574AI� GSM2791574SRX3210857GSM2791574: 43NormPPPoly; Homo sapiens; RNA-SeqGSE104193RNA-SeqTRANSCRIPTOMICcDNAPAIRED - Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2791574AF� GSM2791574SRS2535704%�source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: O111 || replicate: Biological replicate 2@��� GSE104193SRP118788Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ß signalling and malignant features in vitro and in vivo Transcriptome AnalysisWe performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell linesGSE104193A'?6 SRA612618submission brokered by GEOGEO2018-05-10 18:11:11
� <t� �B���R #! ! !� �{- 3 W ! �# �M�A% � 51 3AM � Pat235C.bamSRR61174182017-10-16A�~ A���� AI�8 Pat235CSRX3230155Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat235COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&� Pat235CSRS2554666%�isolate: TEX_235_PrimTum || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�B���R #! ! !� �{- 3 W ! �# �M�A% � 51 3AM � Pat170C.bamSRR61174202017-10-16A�,� B
� AI�7 Pat170CSRX3230153Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat170COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&� Pat170CSRS2554664%�isolate: TEX_170_PrimTum || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�>���R #! ! !� �{- 3 W ! �}# �M�A% � 51 3AM � Pat067N.bamSRR61174232017-10-16A��p BFu� AI�5� Pat067NSRX3230150Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat067NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&� Pat067NSRS2554662%�isolate: TEX_067_Norm || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� 8p� �>���R #! ! !� �{- 3 W ! �}# �M�A% � 51 3AM � Pat224N.bamSRR61174252017-10-16A� �� B o*@ AI�4� Pat224NSRX3230148Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat224NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&� Pat224NSRS2554660%�isolate: TEX_224_Norm || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�B���R #! ! !� �{- 3 W ! �# �M�A% � 51 3AM � Pat044C.bamSRR61174122017-10-16A�` A�G( AI�; Pat044CSRX3230161Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat044COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&� Pat044CSRS2554672%�isolate: TEX_044_PrimTum || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�B���R #! ! !� �{- 3 W ! �# �M�A% � 51 3AM � Pat067C.bamSRR61174092017-10-16A��� A�Ee� AI�<� Pat067CSRX3230164Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat067COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&
Pat067CSRS2554675%�isolate: TEX_067_PrimTum || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� 8_� �O��� R %! ! !� �{ - 3 W ! �# �M�A% � 51 3AM � Pat4005N.bamSRR61174282017-10-16A�k? B ��J� AI�3 Pat4005NSRX3230145Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4005NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat4005NSRS2554657%�isolate: Prospective_4005_ID8_Norm || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�S��� R %! ! !� �{ - 3 W ! � # �M�A% � 51 3AM � Pat4037C.bamSRR61174322017-10-16A��H A�[�� AI�1 Pat4037CSRX3230141Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4037COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG%� Pat4037CSRS2554653%�isolate: Prospective_4037_ID7_PrimTum || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�B���R #! ! !� �{- 3 W ! �# �M�A% � 51 3AM � Pat224M.bamSRR61174242017-10-16A�H,P A���= AI�5 Pat224MSRX3230149Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat224MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat224MSRS2554661%�isolate: TEX_224_Met || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lymph node || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� +V� �P��� R %! ! !� �{ - 3 W ! �# �M�A% � 51 3AM � Pat4024M.bamSRR61174342017-10-16A{Ph` A�Vы AI�0 Pat4024MSRX3230139Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4024MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG%� Pat4024MSRS2554651%�isolate: Prospective_4024_ID19_Met || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�O��� R %! ! !� �{ - 3 W ! �# �M�A% � 51 3AM � Pat4037N.bamSRR61174362017-10-16A�� A���� AI�/ Pat4037NSRX3230137Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4037NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG%� Pat4037NSRS2554649%�isolate: Prospective_4037_ID7_Norm || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�O��� R #! ! !� �{- 3 W ! � # �M�A% � 51 3AM � Pat059C.bamSRR61174112017-10-16A�6�� B��o� AI�;� Pat059CSRX3230162Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat059COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat059CSRS2554673%�isolate: TEX_059_PrimTum || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast (lymph node) || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� *V� �<���#R #! ! !� �{- 3 W ! �y# �M�A% � 51 3AM � Pat235M.bamSRR61174192017-10-16A�� � B p� AI�7� Pat235MSRX3230154Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat235MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat235MSRS2554665%�isolate: TEX_235_Met || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Skin || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�N���"R %! ! !� �{ - 3 W ! �# �M�A% � 51 3AM � Pat4005M.bamSRR61174292017-10-16A�� 8 A�!BW� AI�2� Pat4005MSRX3230144Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4005MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& � Pat4005MSRS2554656%�isolate: Prospective_4005_ID8_Met || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�P���!R %! ! !� �{ - 3 W ! �# �M�A% � 51 3AM � Pat4024N.bamSRR61174332017-10-16A�D�L B
�$�� AI�0� Pat4024NSRX3230140Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4024NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG%�� Pat4024NSRS2554652%�isolate: Prospective_4024_ID19_Norm || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� <t� �=���&R #! ! !� �{- 3 W ! �{# �M�A% � 51 3AM � Pat044M.bamSRR61174132017-10-16A�Up� A��� AI�:� Pat044MSRX3230160Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat044MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat044MSRS2554671%�isolate: TEX_044_Met || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�B���%R #! ! !� �{- 3 W ! �# �M�A% � 51 3AM � Pat066C.bamSRR61174142017-10-16Ay2�� A� � AI�: Pat066CSRX3230159Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat066COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&� Pat066CSRS2554670%�isolate: TEX_066_PrimTum || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�>���$R #! ! !� �{- 3 W ! �}# �M�A% � 51 3AM � Pat235N.bamSRR61174312017-10-16A��S� Bkg� AI�1� Pat235NSRX3230142Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat235NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG%�� Pat235NSRS2554654%�isolate: TEX_235_Norm || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� >z� �=���)R #! ! !� �{- 3 W ! �{# �M�A% � 51 3AM � Pat170M.bamSRR61174212017-10-16A��t� B 6[B� AI�6� Pat170MSRX3230152Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat170MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat170MSRS2554663%�isolate: TEX_170_Met || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�>���(R #! ! !� �{- 3 W ! �}# �M�A% � 51 3AM � Pat059N.bamSRR61174172017-10-16A�7� A��� AI�8� Pat059NSRX3230156Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat059NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat059NSRS2554667%�isolate: TEX_059_Norm || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�<���'R #! ! !� �{- 3 W ! �y# �M�A% � 51 3AM � Pat067M.bamSRR61174222017-10-16A�w� A��M�� AI�6 Pat067MSRX3230151Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat067MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& � Pat067MSRS2554678%�isolate: TEX_067_Met || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lung || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� <i� �O���,R #! ! !� �{- 3 W ! � # �M�A% � 51 3AM � Pat224C.bamSRR61174272017-10-16A n� A�QVT AI�3� Pat224CSRX3230146Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat224COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&� Pat224CSRS2554658%�isolate: TEX_224_PrimTum || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast (lymph node) || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�M���+R %! ! !� �{ - 3 W ! �# �M�A% � 51 3AM � Pat4037M.bamSRR61174372017-10-16A��1` A�+�& AI�.� Pat4037MSRX3230136Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4037MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat4037MSRS2554677%�isolate: Prospective_4037_ID7_Met || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Bone || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�>���*R #! ! !� �{- 3 W ! �}# �M�A% � 51 3AM � Pat066N.bamSRR61174082017-10-16A��9� A��)� AI�= Pat066NSRX3230165Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat066NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&
� Pat066NSRS2554676%�isolate: TEX_066_Norm || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� <c� �B���/R #! ! !� �{- 3 W ! �# �M�A% � 51 3AM � Pat059M.bamSRR61174162017-10-16A��� A�+6� AI�9 Pat059MSRX3230157Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat059MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG&� Pat059MSRS2554668%�isolate: TEX_059_Met || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lymph node || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�S���.R %! ! !� �{ - 3 W ! � # �M�A% � 51 3AM � Pat4005C.bamSRR61174302017-10-16A��� B
�/�@ AI�2 Pat4005CSRX3230143Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4005COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat4005CSRS2554655%�isolate: Prospective_4005_ID8_PrimTum || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�>���-R #! ! !� �{- 3 W ! �}# �M�A% � 51 3AM � Pat044N.bamSRR61174102017-10-16A��C� B<��@ AI�< Pat044NSRX3230163Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat044NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& � Pat044NSRS2554674%�isolate: TEX_044_Norm || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� <b� �=���2R #! ! !� �{- 3 W ! �{# �M�A% � 51 3AM � Pat066M.bamSRR61174152017-10-16Aw��` A�x�[ AI�9� Pat066MSRX3230158Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat066MOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat066MSRS2554669%�isolate: TEX_066_Met || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�T���1R %! ! !� �{ - 3 W ! �!# �M�A% � 51 3AM � Pat4024C.bamSRR61174352017-10-16A�䛈 B���@ AI�/� Pat4024CSRX3230138Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat4024COTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG%�� Pat4024CSRS2554650%�isolate: Prospective_4024_ID19_PrimTum || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11�>���0R #! ! !� �{- 3 W ! �}# �M�A% � 51 3AM � Pat170N.bamSRR61174262017-10-16A� BB��� AI�4 Pat170NSRX3230147Whole Exome Sequencing of breast cancer tumor and metastaseSure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)Pat170NOTHERGENOMICHybrid SelectionPAIRED - ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000AG& Pat170NSRS2554659%�isolate: TEX_179_Norm || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human@��� PRJNA412025SRP119112Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)OtherExome sequencing data from ten metastatic breast cancer patients representing different clinical subtypes and metastatic lesion sites.The patients are part of TEX study (https://clinicaltrials.gov/ct2/show/NCT01433614)Homo sapiensTEX study: https://clinicaltrials.gov/ct2/show/NCT01433614A'M� SRA615716Karolinska InstituteOncology-Pathology2018-05-10 18:11:11
� � � ���9P '! ! ! !!�? ) �Y 3 W ?!! �e e�# A 3AM5 GSM2806527_r1SRR61457732017-10-11A�@ Ar�� GSM2806527AI�� GSM2806527SRX3257822GSM2806527: IgG CLIP-seq in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500GEO Accession: GSM2806527AGy GSM2806527SRS2571283%�source_name: BCBL-1 cells || infected with: Human gammaherpesvirus 8 || clip antibody: IgG (Sigma-Aldrich, Catalog Number I5381) || cell line: BCBL-1 || cell type: primary effusion lymphoma cell line which carries latently infected KSHV@��p GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GSE104711A'C SRA617783submission brokered by GEOGEO2018-05-10 18:11:11
� � �f���:P '! ! ! !!�A ) �Y 3 W ?!! �u e�# A 3AM5� GSM2806528_r1SRR61457742017-10-11A�3�8 A��� GSM2806528AI� GSM2806528SRX3257823GSM2806528: K8 CLIP-seq-1 in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500GEO Accession: GSM2806528AGy� GSM2806528SRS2571284%�source_name: BCBL-1 cells || infected with: Human gammaherpesvirus 8 || clip antibody: K8 (generated and purified in our lab; Yan Wang, et al.,J Viral, 2011 and Xin Wang, et al., PLOS pathogens, 2015) || cell line: BCBL-1 || cell type: primary effusion lymphoma cell line which carries latently infected KSHV@��p GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GSE104711A'C SRA617783submission brokered by GEOGEO2018-05-10 18:11:11
� � �f���;P '! ! ! !!�A ) �Y 3 W ?!! �u e�# A 3AM6 GSM2806529_r1SRR61457752017-10-11A�vv8 A��e� GSM2806529AI�� GSM2806529SRX3257824GSM2806529: K8 CLIP-seq-2 in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-SeqGSE104711RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500GEO Accession: GSM2806529AGz GSM2806529SRS2571285%�source_name: BCBL-1 cells || infected with: Human gammaherpesvirus 8 || clip antibody: K8 (generated and purified in our lab; Yan Wang, et al.,J Viral, 2011 and Xin Wang, et al., PLOS pathogens, 2015) || cell line: BCBL-1 || cell type: primary effusion lymphoma cell line which carries latently infected KSHV@��p GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GSE104711A'C SRA617783submission brokered by GEOGEO2018-05-10 18:11:11
�x���<P '! ! ! !!� ) �Y 3 W ?!! �S e�# A 3AM6� GSM2806530_r1SRR61457762017-10-11AJ}� A�H@ GSM2806530AI� GSM2806530SRX3257825GSM2806530: K8 CLIP-seq in BJAB cells; Homo sapiens; RIP-SeqGSE104711RIP-SeqTRANSCRIPTOMICotherSINGLE - Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.ILLUMINAIllumina HiSeq 2500INSTRUMENT_MODEL: Illumina HiSeq 2500GEO Accession: GSM2806530AGz� GSM2806530SRS2571286%�source_name: BJAB cells || clip antibody: K8 (generated and purified in our lab; Yan Wang, et al.,J Viral, 2011 and Xin Wang, et al., PLOS pathogens, 2015) || cell line: BJAB || cell type: KSHV-free Burkitt lymphoma B cell line@��p GSE104711SRP119540K8 CLIP-Seq in KSHV reactivated BCBL-1 cellsOtherKSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.GSE104711A'C SRA617783submission brokered by GEOGEO2018-05-10 18:11:11
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v� ����cP '! ! ! !!o ) �A 3 W ?!! � �E9�# A 3AM� GSM2806581_r1SRR61470762017-10-11Ar3 A��Y{ GSM2806581AI�� GSM2806581SRX3259125GSM2806581: EtOH_11hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806581AGE� GSM2806581SRS2572558%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 11 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����bP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM� GSM2806577_r1SRR61470722017-10-11AxX� A�fܩ GSM2806577AI�� GSM2806577SRX3259121GSM2806577: EtOH_7hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806577AGC� GSM2806577SRS2572554%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 7 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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v� ����eP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM� GSM2806571_r1SRR61470662017-10-11AzP� A��!� GSM2806571AI�� GSM2806571SRX3259115GSM2806571: EtOH_1hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806571AG@� GSM2806571SRS2572548%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 1 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����dP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM� GSM2806573_r1SRR61470682017-10-11Av�(` A�5 ,� GSM2806573AI�� GSM2806573SRX3259117GSM2806573: EtOH_3hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806573AGA� GSM2806573SRS2572550%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 3 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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t� ����gP '! ! ! !!m ) �A 3 W ?!! �% �E9�# A 3AM GSM2806570_r1SRR61470652017-10-11Ay�` A��X� GSM2806570AI�ހ GSM2806570SRX3259114GSM2806570: DEX_11hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806570AG@ GSM2806570SRS2572547%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 11 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����fP '! ! ! !!o ) �A 3 W ?!! � �E9�# A 3AM GSM2806582_r1SRR61470772017-10-11AuH` A��� GSM2806582AI�� GSM2806582SRX3259126GSM2806582: EtOH_11hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806582AGF GSM2806582SRS2572559%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 11 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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t� ����iP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM�� GSM2806561_r1SRR61470562017-10-11Av��` A�
�(� GSM2806561AI�� GSM2806561SRX3259105GSM2806561: DEX_3hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806561AG;� GSM2806561SRS2572538%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 3 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����hP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM�� GSM2806563_r1SRR61470582017-10-11Au� A��_) GSM2806563AI�� GSM2806563SRX3259107GSM2806563: DEX_5hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806563AG<� GSM2806563SRS2572540%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 5 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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r� ����kP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM GSM2806576_r1SRR61470712017-10-11A{sQ A��䥀 GSM2806576AI�� GSM2806576SRX3259120GSM2806576: EtOH_5hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806576AGC GSM2806576SRS2572553%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 5 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����jP '! ! ! !!m ) �A 3 W ?!! �% �E9�# A 3AM� GSM2806569_r1SRR61470642017-10-11Az)L� A���) GSM2806569AI�� GSM2806569SRX3259113GSM2806569: DEX_11hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806569AG?� GSM2806569SRS2572546%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 11 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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t� ����mP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM� GSM2806560_r1SRR61470552017-10-11ApVO� A� �M GSM2806560AI�ـ GSM2806560SRX3259104GSM2806560: DEX_1hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806560AG; GSM2806560SRS2572537%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 1 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����lP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM GSM2806568_r1SRR61470632017-10-11A�ڠ A�o&7� GSM2806568AI�݀ GSM2806568SRX3259112GSM2806568: DEX_9hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806568AG? GSM2806568SRS2572545%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 9 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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v� ����oP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM� GSM2806575_r1SRR61470702017-10-11Au�J� A�y�� GSM2806575AI�� GSM2806575SRX3259119GSM2806575: EtOH_5hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806575AGB� GSM2806575SRS2572552%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 5 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����nP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM GSM2806574_r1SRR61470692017-10-11A{d�� A��!�� GSM2806574AI�� GSM2806574SRX3259118GSM2806574: EtOH_3hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806574AGB GSM2806574SRS2572551%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 3 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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t� ����qP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM GSM2806572_r1SRR61470672017-10-11AU� A�k GSM2806572AI�߀ GSM2806572SRX3259116GSM2806572: EtOH_1hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806572AGA GSM2806572SRS2572549%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 1 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����pP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM� GSM2806567_r1SRR61470622017-10-11ApO:@ A�D� GSM2806567AI�� GSM2806567SRX3259111GSM2806567: DEX_9hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806567AG>� GSM2806567SRS2572544%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 9 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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t� ����sP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM� GSM2806579_r1SRR61470742017-10-11Ay> A� j}� GSM2806579AI�� GSM2806579SRX3259123GSM2806579: EtOH_9hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806579AGD� GSM2806579SRS2572556%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 9 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����rP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM GSM2806564_r1SRR61470592017-10-11Au�` A�| 8� GSM2806564AI�ۀ GSM2806564SRX3259108GSM2806564: DEX_5hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806564AG= GSM2806564SRS2572541%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 5 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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v� ����uP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM � GSM2806565_r1SRR61470602017-10-11Ay��� A�|&b� GSM2806565AI�� GSM2806565SRX3259109GSM2806565: DEX_7hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806565AG=� GSM2806565SRS2572542%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 7 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����tP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM GSM2806580_r1SRR61470752017-10-11Av�k A� �D GSM2806580AI�� GSM2806580SRX3259124GSM2806580: EtOH_9hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806580AGE GSM2806580SRS2572557%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 9 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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t� ����wP '! ! ! !!m ) �A 3 W ?!! � �E9�# A 3AM GSM2806578_r1SRR61470732017-10-11Awx� AҴD( GSM2806578AI�� GSM2806578SRX3259122GSM2806578: EtOH_7hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806578AGD GSM2806578SRS2572555%�source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 7 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����vP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM GSM2806566_r1SRR61470612017-10-11Ar��@ A͑�� GSM2806566AI�܀ GSM2806566SRX3259110GSM2806566: DEX_7hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806566AG> GSM2806566SRS2572543%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 7 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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t� ����yP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM�� GSM2806559_r1SRR61470542017-10-11AxRR� A�a�� GSM2806559AI�� GSM2806559SRX3259103GSM2806559: DEX_1hr_Rep1; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806559AG:� GSM2806559SRS2572536%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 1 hr || biological replicate: 1@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11����xP '! ! ! !!k ) �A 3 W ?!! �# �E9�# A 3AM� GSM2806562_r1SRR61470572017-10-11Az%�@ A��� GSM2806562AI�ڀ GSM2806562SRX3259106GSM2806562: DEX_3hr_Rep2; Homo sapiens; RNA-SeqGSE104714RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806562AG< GSM2806562SRS2572539%�source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 3 hr || biological replicate: 2@��� GSE104714SRP119557Clustering gene expression time series data using an infinite Gaussian process mixture modelTranscriptome AnalysisIn order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.GSE104714A'C. SRA617809submission brokered by GEOGEO2018-05-10 18:11:11
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T� �&���P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM;� GSM2806596_r1SRR61479932017-10-11AN�� A�ׄ GSM2806596AI� � GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806596AGf� GSM2806596SRS2573349o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�&���P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM8 GSM2806594_r2SRR61479862017-10-11AN�� A�ׄ GSM2806594AI� � GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806594AGf GSM2806594SRS2573348o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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B� �&���P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM<� GSM2806596_r3SRR61479952017-10-11AN�� A�ׄ GSM2806596AI� � GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806596AGf� GSM2806596SRS2573349o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�8���P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM0 GSM2806590_r2SRR61479702017-10-11AN�� A�ׄ GSM2806590AI� � GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806590AGd GSM2806590SRS2573344o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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T� �&��� P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM< GSM2806596_r2SRR61479942017-10-11AN�� A�ׄ GSM2806596AI� � GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806596AGf� GSM2806596SRS2573349o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�&���P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM:� GSM2806595_r3SRR61479912017-10-11AN�� A�ׄ GSM2806595AI� GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806595AGg GSM2806595SRS2573350o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806591AGd� GSM2806591SRS2573345o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�8��� P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM2� GSM2806591_r3SRR61479752017-10-11AN�� A�ׄ GSM2806591AI�
GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806591AGd� GSM2806591SRS2573345o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806591AGd� GSM2806591SRS2573345o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�&��� P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM; GSM2806595_r4SRR61479922017-10-11AN�� A�ׄ GSM2806595AI� GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806595AGg GSM2806595SRS2573350o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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T� �&���"P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM8� GSM2806594_r3SRR61479872017-10-11AN�� A�ׄ GSM2806594AI� � GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806594AGf GSM2806594SRS2573348o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�&���!P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM5� GSM2806593_r1SRR61479812017-10-11AN�� A�ׄ GSM2806593AI� GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806593AGe� GSM2806593SRS2573347o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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T� �8���$P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM0� GSM2806590_r3SRR61479712017-10-11AN�� A�ׄ GSM2806590AI� � GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806590AGd GSM2806590SRS2573344o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�&���#P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM9� GSM2806595_r1SRR61479892017-10-11AN�� A�ׄ GSM2806595AI� GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806595AGg GSM2806595SRS2573350o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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� GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806592AGe GSM2806592SRS2573346o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�&���%P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM6 GSM2806593_r2SRR61479822017-10-11AN�� A�ׄ GSM2806593AI� GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806593AGe� GSM2806593SRS2573347o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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B� �&���(P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM: GSM2806595_r2SRR61479902017-10-11AN�� A�ׄ GSM2806595AI� GSM2806595SRX3260014GSM2806595: K96243_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806595AGg GSM2806595SRS2573350o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�8���'P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM4 GSM2806592_r2SRR61479782017-10-11AN�� A�ׄ GSM2806592AI�
� GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806592AGe GSM2806592SRS2573346o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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B� �&���*P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM6� GSM2806593_r3SRR61479832017-10-11AN�� A�ׄ GSM2806593AI� GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806593AGe� GSM2806593SRS2573347o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�8���)P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM5 GSM2806592_r4SRR61479802017-10-11AN�� A�ׄ GSM2806592AI�
� GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806592AGe GSM2806592SRS2573346o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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T� �8���,P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM/ GSM2806589_r4SRR61479682017-10-11AN�� A�ׄ GSM2806589AI� GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806589AGc� GSM2806589SRS2573343o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�&���+P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM9 GSM2806594_r4SRR61479882017-10-11AN�� A�ׄ GSM2806594AI� � GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806594AGf GSM2806594SRS2573348o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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T� �&���.P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM7� GSM2806594_r1SRR61479852017-10-11AN�� A�ׄ GSM2806594AI� � GSM2806594SRX3260013GSM2806594: K96243_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806594AGf GSM2806594SRS2573348o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�&���-P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM7 GSM2806593_r4SRR61479842017-10-11AN�� A�ׄ GSM2806593AI� GSM2806593SRX3260012GSM2806593: K96243_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806593AGe� GSM2806593SRS2573347o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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GSM2806591SRX3260010GSM2806591: DDL3431_3; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806591AGd� GSM2806591SRS2573345o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�8���/P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM.� GSM2806589_r3SRR61479672017-10-11AN�� A�ׄ GSM2806589AI� GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806589AGc� GSM2806589SRS2573343o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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B� �8���2P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM-� GSM2806589_r1SRR61479652017-10-11AN�� A�ׄ GSM2806589AI� GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806589AGc� GSM2806589SRS2573343o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�8���1P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM. GSM2806589_r2SRR61479662017-10-11AN�� A�ׄ GSM2806589AI� GSM2806589SRX3260008GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806589AGc� GSM2806589SRS2573343o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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B� �&���4P '! ! ! !!} ) �A 3 W ?!! � �/9� A 3AM= GSM2806596_r4SRR61479962017-10-11AN�� A�ׄ GSM2806596AI� � GSM2806596SRX3260015GSM2806596: K96243_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806596AGf� GSM2806596SRS2573349o"source_name: Wild type || strain: K96243 || genotype: Wild type@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�8���3P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM/� GSM2806590_r1SRR61479692017-10-11AN�� A�ׄ GSM2806590AI� � GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806590AGd GSM2806590SRS2573344o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
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B� �8���6P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM1 GSM2806590_r4SRR61479722017-10-11AN�� A�ׄ GSM2806590AI� � GSM2806590SRX3260009GSM2806590: DDL3431_2; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806590AGd GSM2806590SRS2573344o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11�8���5P '! ! ! !! ) �A 3 W ?!! �- �/9� A 3AM3� GSM2806592_r1SRR61479772017-10-11AN�� A�ׄ GSM2806592AI�
� GSM2806592SRX3260011GSM2806592: DDL3431_4; Burkholderia pseudomallei; RNA-SeqGSE104716RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions. Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806592AGe GSM2806592SRS2573346o"source_name: TctR mutant || strain: K96243::delta(tctR) || genotype: TctR mutant@��0 GSE104716SRP119575RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretionTranscriptome AnalysisWe report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters. Overall design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.GSE104716A'CF SRA617842submission brokered by GEOGEO2018-05-10 18:11:11
� �� �3���P '! ! ! !!u ) �; 3 W ?!! �- �%9� A 3AM� GSM2806691_r1SRR61487292017-10-11Agv� A��� GSM2806691AI�O� GSM2806691SRX3260749GSM2806691: CD3/28+cGAMP_3h_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806691AG� GSM2806691SRS2574059'jsource_name: helper T cell_CD3/28+cGAMP_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 3hrs@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11�$���P '! ! ! !!k ) �; 3 W ?!! � �%9� A 3AM�� GSM2806692_r1SRR61487302017-10-11Aij�� A�u�� GSM2806692AI�P GSM2806692SRX3260750GSM2806692: CD3/28_24h_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806692AG� GSM2806692SRS2574060'jsource_name: helper T cell_CD3/28_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28 for 24hrs@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
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?�� GSM2806686AI�M GSM2806686SRX3260744GSM2806686: Naive CD4_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806686AG� GSM2806686SRS2574058'jsource_name: helper T cell_Naive CD4 || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: none (naïve)@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11�3��� P '! ! ! !!u ) �; 3 W ?!! �- �%9� A 3AM� GSM2806690_r1SRR61487282017-10-11Adی@ A��.� GSM2806690AI�O GSM2806690SRX3260748GSM2806690: CD3/28+cGAMP_3h_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806690AG� GSM2806690SRS2574064'jsource_name: helper T cell_CD3/28+cGAMP_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 3hrs@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
� �� �!��� P '! ! ! !!i ) �; 3 W ?!! � �%9� A 3AM GSM2806689_r1SRR61487272017-10-11AZӐ� A���� GSM2806689AI�N� GSM2806689SRX3260747GSM2806689: CD3/28_3h_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806689AG� GSM2806689SRS2574057'jsource_name: helper T cell_CD3/28_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28 for 3hrs@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11�6��� P '! ! ! !!w ) �; 3 W ?!! �1 �%9� A 3AM�� GSM2806694_r1SRR61487322017-10-11Ao� A�:\l GSM2806694AI�Q GSM2806694SRX3260752GSM2806694: CD3/28+cGAMP_24h_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806694AG� GSM2806694SRS2574062'jsource_name: helper T cell_CD3/28+cGAMP_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 24hrs@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
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�p A�h[}� GSM2806687AI�M� GSM2806687SRX3260745GSM2806687: Naive CD4_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806687AG� GSM2806687SRS2574056'jsource_name: helper T cell_Naive CD4 || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: none (naïve)@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11�6���
P '! ! ! !!w ) �; 3 W ?!! �1 �%9� A 3AM� GSM2806695_r1SRR61487332017-10-11Ag��� A�%~v GSM2806695AI�Q� GSM2806695SRX3260753GSM2806695: CD3/28+cGAMP_24h_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806695AG� GSM2806695SRS2574063'jsource_name: helper T cell_CD3/28+cGAMP_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28+cGAMP for 24hrs@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
� �� �$���P '! ! ! !!k ) �; 3 W ?!! � �%9� A 3AM� GSM2806693_r1SRR61487312017-10-11Aa�@� A� �W GSM2806693AI�P� GSM2806693SRX3260751GSM2806693: CD3/28_24h_2; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806693AG� GSM2806693SRS2574061'jsource_name: helper T cell_CD3/28_24h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28 for 24hrs@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11�!���P '! ! ! !!i ) �; 3 W ?!! � �%9� A 3AM~� GSM2806688_r1SRR61487262017-10-11AeX� A�'gڀ GSM2806688AI�N GSM2806688SRX3260746GSM2806688: CD3/28_3h_1; Mus musculus; RNA-SeqGSE104725RNA-SeqTRANSCRIPTOMICcDNASINGLE - RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocolsILLUMINAIllumina HiSeq 1500INSTRUMENT_MODEL: Illumina HiSeq 1500GEO Accession: GSM2806688AG� GSM2806688SRS2574055'jsource_name: helper T cell_CD3/28_3h || strain: C57BL/6 || tissue: spleen || age: 12 weeks || genotype: wild type || cell type: helper T cell; CD4+ T cells || stimulated with: anti-CD3/28 for 3hrs@��� GSE104725SRP119595Quantitative Transcriptome Analysis of T cells stimulated with STING ligandsTranscriptome AnalysisSTING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce type I IFN responses like innate immune cells. Overall design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.GSE104725A'CR SRA617887submission brokered by GEOGEO2018-05-10 18:11:11
" �" �i���|P '! ! ! !!w ) �g 3 W ?!! � �9� A 3AM� GSM2806883_r1SRR61503672017-10-11A|w� A��)@ GSM2806883AI� GSM2806883SRX3262385GSM2806883: Liver - TCPOBOP K8; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806883AGF GSM2806883SRS2575313'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11�i���{P '! ! ! !!w ) �g 3 W ?!! � �9� A 3AM� GSM2806884_r1SRR61503682017-10-11A{Z�� A�;�� GSM2806884AI貀 GSM2806884SRX3262386GSM2806884: Liver - TCPOBOP K9; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806884AGF� GSM2806884SRS2575314'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
� �k���~P '! ! ! !!{ ) �g 3 W ?!! � �9� A 3AM߀ GSM2806877_r1SRR61503612017-10-11A{�p A�d � GSM2806877AI� GSM2806877SRX3262379GSM2806877: Liver - Corn Oil KS2; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806877AGC GSM2806877SRS2575307'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11�k���}P '! ! ! !!{ ) �g 3 W ?!! � �9� A 3AM� GSM2806878_r1SRR61503622017-10-11A|Ӱ� A�D�]� GSM2806878AI诀 GSM2806878SRX3262380GSM2806878: Liver - Corn Oil KS3; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806878AGC� GSM2806878SRS2575308'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
( �( �f��� P '! ! ! !!q ) �g 3 W ?!! � �9� A 3AM� GSM2806881_r1SRR61503652017-10-11Az �0 A�N�� GSM2806881AI� GSM2806881SRX3262383GSM2806881: Liver - PCN KS6; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806881AGE GSM2806881SRS2575311'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11�f���P '! ! ! !!q ) �g 3 W ?!! � �9� A 3AM� GSM2806879_r1SRR61503632017-10-11A�W�� A��?Ā GSM2806879AI� GSM2806879SRX3262381GSM2806879: Liver - PCN KS4; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806879AGD GSM2806879SRS2575309'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
% �% �f���P '! ! ! !!q ) �g 3 W ?!! � �9� A 3AM� GSM2806880_r1SRR61503642017-10-11A K� A�҉d� GSM2806880AI谀 GSM2806880SRX3262382GSM2806880: Liver - PCN KS5; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806880AGD� GSM2806880SRS2575310'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11�i���P '! ! ! !!w ) �g 3 W ?!! � �9� A 3AM� GSM2806882_r1SRR61503662017-10-11Ay�u� A�*� GSM2806882AI豀 GSM2806882SRX3262384GSM2806882: Liver - TCPOBOP K7; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806882AGE� GSM2806882SRS2575312'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
� � �k���P '! ! ! !!{ ) �g 3 W ?!! � �9� A 3AM� GSM2806876_r1SRR61503602017-10-11Av��� A��t GSM2806876AI讀 GSM2806876SRX3262378GSM2806876: Liver - Corn Oil KS1; Mus musculus; RNA-SeqGSE104734RNA-SeqTRANSCRIPTOMICcDNAPAIRED - RNA was extracted using RNA zol Bee reagent (Tel Test Inc) Illumina RNA-Seq library preparation The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806876AGB� GSM2806876SRS2575306'jsource_name: Liver || strain: C57BL/6 || genotype: wild type@��� GSE104734SRP119609RNA-Seq Profiling of Pharmacological Activation of PXR and CAR MiceTranscriptome AnalysisThis study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq Overall design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.GSE104734A'CZ SRA617912submission brokered by GEOGEO2018-05-10 18:11:11
9 9 �A���.P '! ! ! !! ) �1 3 W ?!! � �9�m A 3AM� GSM2806924_r1SRR61504152017-10-11A`�A� A�{��� GSM2806924AI� GSM2806924SRX3262427GSM2806924: ATCC27064; Streptomyces clavuligerus; RNA-SeqGSE104738RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806924AGG GSM2806924SRS2575351�wsource_name: mycelium || phenotype: wildtype || strain: ATCC 27064 || type-material: type strain of Streptomyces clavuligerus@��� GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGSE104738A'C\ SRA617916submission brokered by GEOGEO2018-05-10 18:11:11
s s ����/P '! ! ! !!y ) �1 3 W ?!! � �9�m A 3AM� GSM2806925_r2SRR61504182017-10-11A^=� AǗ�w� GSM2806925AI賀 GSM2806925SRX3262428GSM2806925: F613-1; Streptomyces clavuligerus; RNA-SeqGSE104738RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806925AGG� GSM2806925SRS2575352msource_name: mycelium || phenotype: industrial strain || strain: F613-1@��� GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGSE104738A'C\ SRA617916submission brokered by GEOGEO2018-05-10 18:11:11
9 9 �A���0P '! ! ! !! ) �1 3 W ?!! � �9�m A 3AM� GSM2806924_r2SRR61504162017-10-11A`�A� A�{^ GSM2806924AI� GSM2806924SRX3262427GSM2806924: ATCC27064; Streptomyces clavuligerus; RNA-SeqGSE104738RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806924AGG GSM2806924SRS2575351�wsource_name: mycelium || phenotype: wildtype || strain: ATCC 27064 || type-material: type strain of Streptomyces clavuligerus@��� GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGSE104738A'C\ SRA617916submission brokered by GEOGEO2018-05-10 18:11:11
s s ����1P '! ! ! !!y ) �1 3 W ?!! � �9�m A 3AM� GSM2806925_r1SRR61504172017-10-11A^=� AǗ�� GSM2806925AI賀 GSM2806925SRX3262428GSM2806925: F613-1; Streptomyces clavuligerus; RNA-SeqGSE104738RNA-SeqTRANSCRIPTOMICcDNASINGLE - the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).ILLUMINAIllumina HiSeq 2000INSTRUMENT_MODEL: Illumina HiSeq 2000GEO Accession: GSM2806925AGG� GSM2806925SRS2575352msource_name: mycelium || phenotype: industrial strain || strain: F613-1@��� GSE104738SRP119613The compact genome in the clavulanic acid producing Streptomyces strain unravels a variety of horizontal transfer reservoirsTranscriptome AnalysisBacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes. Overall design: mRNA profiles of S. clavuligerus F613-1 and ATCC27064 strains were generated by deep sequencingGSE104738A'C\ SRA617916submission brokered by GEOGEO2018-05-10 18:11:11
U �U �z���S ! ! ! E! _�} �5 � #�
� �+ �G 3AM�� SRR62140602017-10-25A��fH B w|�� AJ�+� SRX3322823A@� ENCODE biosample ENCBS195LAYSRS1860811%�Homo sapiens MCF-7 immortalized cell lineENCBS195LAY at ENCODE: https://www.encodeproject.org/ENCBS195LAY/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdfdev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'�� SRA6241032018-05-10 18:11:11�%���Q ! ! ! ! � #�
� �+ �G 3AM� SRR62140592017-10-25A��Tx B�Ħ� AJ�+ SRX3322822AG�� SRS2627513@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'�� SRA6241032018-05-10 18:11:11
+ + �O���ES ! ! ! E! _�' �5 � #�
� �+ �G 3AM� SRR62141072017-10-25A�� A��
� AJ�C SRX3322868A@�� ENCODE biosample ENCBS200IWRSRS1860706%�Homo sapiens MCF-7 immortalized cell lineENCBS200IWR at ENCODE: https://www.encodeproject.org/ENCBS200IWR/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'�� SRA6241352018-05-10 18:11:11
+ + �O���FS ! ! ! E! _�' �5 � #�
� �+ �G 3AM�� SRR62141082017-10-25A�J� A��� AJ�C� SRX3322869A@� ENCODE biosample ENCBS488MMMSRS1860859%�Homo sapiens MCF-7 immortalized cell lineENCBS488MMM at ENCODE: https://www.encodeproject.org/ENCBS488MMM/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'�� SRA6241352018-05-10 18:11:11
+ + �O��� S ! ! ! E! _�' �5 � #�
� �+ �G 3AM�1� SRR62141962017-10-25A��X A���^� AJ�]� SRX3322943A@�� ENCODE biosample ENCBS200IWRSRS1860706%�Homo sapiens MCF-7 immortalized cell lineENCBS200IWR at ENCODE: https://www.encodeproject.org/ENCBS200IWR/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'� SRA6241702018-05-10 18:11:11
+ + �O���
S ! ! ! E! _�' �5 � #�
� �+ �G 3AM�1 SRR62141952017-10-25A�-�� A���V` AJ�] SRX3322942A@�� ENCODE biosample ENCBS609QTYSRS1860691%�Homo sapiens MCF-7 immortalized cell lineENCBS609QTY at ENCODE: https://www.encodeproject.org/ENCBS609QTY/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'� SRA6241702018-05-10 18:11:11
� � �z��� S ! ! ! E! _�} �5 � #�
� �+ �G 3AM�2� SRR62141982017-10-25A~�2� A�9f$� AJ�^� SRX3322945A@�� ENCODE biosample ENCBS110CZNSRS1860750%�Homo sapiens MCF-7 immortalized cell lineENCBS110CZN at ENCODE: https://www.encodeproject.org/ENCBS110CZN/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdfdev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'� SRA6241712018-05-10 18:11:11
� � �z��� S ! ! ! E! _�} �5 � #�
� �+ �G 3AM�2 SRR62141972017-10-25A|Ys� A�^�b AJ�^ SRX3322944A@�� ENCODE biosample ENCBS764AUTSRS1860751%�Homo sapiens MCF-7 immortalized cell lineENCBS764AUT at ENCODE: https://www.encodeproject.org/ENCBS764AUT/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdfdev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'� SRA6241712018-05-10 18:11:11
+ + �O��� S ! ! ! E! _�' �5 � #�
� �+ �G 3AM�|� SRR62143462017-10-25Ay�P A�{`s AJ��� SRX3323023A@�� ENCODE biosample ENCBS200IWRSRS1860706%�Homo sapiens MCF-7 immortalized cell lineENCBS200IWR at ENCODE: https://www.encodeproject.org/ENCBS200IWR/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || cell line: MCF-7 || sex: female || sample type: immortalized cell line || donor ID: ENCDO000AAE || age: 69 year || health state: breast cancer (adenocarcinoma) || lab: Michael Snyder, Stanford@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'�� SRA6242242018-05-10 18:11:11
+ + �O��� S ! ! ! E! _�' �5 � #�
� �+ �G 3AM�| SRR62143452017-10-25At��� A�_K�@ AJ�� SRX3323022A@�]� ENCODE biosample ENCBS547AXBSRS1860470%�Homo sapiens MCF-7 immortalized cell lineENCBS547AXB at ENCODE: https://www.encodeproject.org/ENCBS547AXB/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'�� SRA6242242018-05-10 18:11:11
+ + �O���yS ! ! ! E! _�' �5 � #�
� �+ �G 3AMߞ SRR62144132017-10-25A�Ka� A����� AJ��� SRX3323089A@� ENCODE biosample ENCBS488MMMSRS1860859%�Homo sapiens MCF-7 immortalized cell lineENCBS488MMM at ENCODE: https://www.encodeproject.org/ENCBS488MMM/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'�� SRA6242692018-05-10 18:11:11
� + � �g���MO ! ! ! ! U �# � �7% 3AM� SRR62400662017-10-31AC� � A�[ � AJ�b SRX3347394AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�O���zS ! ! ! E! _�' �5 � #�
� �+ �G 3AMߞ� SRR62144142017-10-25A�>� A��G�` AJ�� SRX3323090A@鍀 ENCODE biosample ENCBS670IYVSRS1860582%�Homo sapiens MCF-7 immortalized cell lineENCBS670IYV at ENCODE: https://www.encodeproject.org/ENCBS670IYV/ || Derived from ENCODE donor ENCDO000AAE: https://www.encodeproject.org/ENCDO000AAE/ || growth protocol: https://www.encodeproject.org/documents/2a32df77-1325-4a2d-af71-2f2b68eb9830/@@download/attachment/Snyder_MCF7%20Cell%20Growth%20Protocol.pdf || ENCODE dbxrefs Cellosaurus CVCL_0031: http://web.expasy.org/cellosaurus/CVCL_0031dev stage: adult || donor ID: ENCDO000AAE || age: 69 year || sex: female || lab: Michael Snyder, Stanford || health state: breast cancer (adenocarcinoma) || sample type: immortalized cell line || cell line: MCF-7@�� GSE59395SRP012412GSE59395: Genome-wide map of regulatory interactions in the human genomeEpigeneticsSummary: We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications, RAD21 and RNAPII in K562 cell line, two biological replicates each.GSE59395: Genome-wide map of regulatory interactions in the human genomeGEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = [email protected]; Institute = ENCODE DCC; Address = 300 Pasteur Dr; City = Stanford; Zip/Postal Code = 94305-5120; Country = USA || Project Contributor: Nastaran, Heidari || Project Contributor: Doug, H, Phanstiel || Project Contributor: Chao, He || Project Contributor: Fabian, Grubert || Project Contributor: Fereshteh, Jahanbani || Project Contributor: Maya, Kasowski || Project Contributor: Michael, Q, Zhang || Project Contributor: Michael, P, SnyderA'�� SRA6242692018-05-10 18:11:11
& �& �g���OO ! ! ! ! U �# � �7% 3AM� SRR62400402017-10-31AA2!� A�k�� AJ�o SRX3347420AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���NO ! ! ! ! U �# � �7% 3AM� SRR62400342017-10-31A4x$ A�N�� AJ�r SRX3347426AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���QO ! ! ! ! U �# � �7% 3AM� SRR62400532017-10-31A9w� A�>� AJ�h� SRX3347407AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���PO ! ! ! ! U �# � �7% 3AM� SRR62400282017-10-31A@*ڀ A�2�x AJ�u SRX3347432AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���SO ! ! ! ! U �# � �7% 3AM� SRR62400712017-10-31A7�� A�j\P AJ�_� SRX3347389AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���RO ! ! ! ! U �# � �7% 3AM� SRR62400512017-10-31A<�� A�� AJ�i� SRX3347409AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���UO ! ! ! ! U �# � �7% 3AM� SRR62400192017-10-31A<�F A�I� AJ�y� SRX3347441AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���TO ! ! ! ! U �# � �7% 3AM� SRR62400352017-10-31A: A���� AJ�q� SRX3347425AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���WO ! ! ! ! U �# � �7% 3AM� SRR62400472017-10-31A=y. A��P AJ�k� SRX3347413AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���VO ! ! ! ! U �# � �7% 3AM� SRR62400462017-10-31A2� A�qD� AJ�l SRX3347414AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���YO ! ! ! ! U �# � �7% 3AM� SRR62400302017-10-31A>E A��� AJ�t SRX3347430AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���XO ! ! ! ! U �# � �7% 3AM� SRR62400562017-10-31A;�S A���H AJ�g SRX3347404AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���[O ! ! ! ! U �# � �7% 3AM� SRR62400522017-10-31A?�; A��� AJ�i SRX3347408AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���ZO ! ! ! ! U �# � �7% 3AM� SRR62400542017-10-31AL�s� A� \� AJ�h SRX3347406AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���]O ! ! ! ! U �# � �7% 3AM� SRR62400642017-10-31AH �� A�� � AJ�c SRX3347396AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���\O ! ! ! ! U �# � �7% 3AM� SRR62400332017-10-31AB� A�B�� AJ�r� SRX3347427AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���_O ! ! ! ! U �# � �7% 3AM� SRR62400372017-10-31A?8v A��� AJ�p� SRX3347423AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���^O ! ! ! ! U �# � �7% 3AM� SRR62400732017-10-31AA�� A���@ AJ�^� SRX3347387AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���aO ! ! ! ! U �# � �7% 3AM� SRR62400292017-10-31AA0N� A�i]8 AJ�t� SRX3347431AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���`O ! ! ! ! U �# � �7% 3AM� SRR62400742017-10-31A<�5 A��x AJ�^ SRX3347386AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���cO ! ! ! ! U �# � �7% 3AM� SRR62400682017-10-31A0"� A�)N� AJ�a SRX3347392AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���bO ! ! ! ! U �# � �7% 3AM� SRR62400182017-10-31A9X8 A� AJ�z SRX3347442AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���eO ! ! ! ! U �# � �7% 3AM� SRR62400422017-10-31A@� A� �� AJ�n SRX3347418AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���dO ! ! ! ! U �# � �7% 3AM� SRR62400312017-10-31A3! A���0 AJ�s� SRX3347429AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���gO ! ! ! ! U �# � �7% 3AM� SRR62400212017-10-31A@�u A���� AJ�x� SRX3347439AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���fO ! ! ! ! U �# � �7% 3AM� SRR62400222017-10-31A5Ӄ A��+� AJ�x SRX3347438AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���iO ! ! ! ! U �# � �7% 3AM� SRR62400592017-10-31A5�� A���� AJ�e� SRX3347401AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���hO ! ! ! ! U �# � �7% 3AM� SRR62400452017-10-31A4�
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���kO ! ! ! ! U �# � �7% 3AM� SRR62400652017-10-31A=�4 A���� AJ�b� SRX3347395AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���jO ! ! ! ! U �# � �7% 3AM� SRR62400602017-10-31ACp6 A�@ AJ�e SRX3347400AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���mO ! ! ! ! U �# � �7% 3AM� SRR62400752017-10-31A8Q� A��8� AJ�]� SRX3347385AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���lO ! ! ! ! U �# � �7% 3AM� SRR62400722017-10-31AAZ! A��0 AJ�_ SRX3347388AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���oO ! ! ! ! U �# � �7% 3AM� SRR62400612017-10-31AA�M� A�� AJ�d� SRX3347399AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���nO ! ! ! ! U �# � �7% 3AM� SRR62400322017-10-31AA�ހ A�Y�8 AJ�s SRX3347428AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���qO ! ! ! ! U �# � �7% 3AM� SRR62400622017-10-31AB�Ӏ A�'K( AJ�d SRX3347398AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���pO ! ! ! ! U �# � �7% 3AM� SRR62400262017-10-31ABe�� A�؍X AJ�v SRX3347434AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���sO ! ! ! ! U �# � �7% 3AM� SRR62400702017-10-31A3
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���rO ! ! ! ! U �# � �7% 3AM� SRR62400492017-10-31A>� A�Xa� AJ�j� SRX3347411AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���uO ! ! ! ! U �# � �7% 3AM� SRR62400582017-10-31A@倀 A��� AJ�f SRX3347402AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���tO ! ! ! ! U �# � �7% 3AM� SRR62400502017-10-31A6�C A��/� AJ�j SRX3347410AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���wO ! ! ! ! U �# � �7% 3AM� SRR62400142017-10-31A4�� A���@ AJ�| SRX3347446AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���vO ! ! ! ! U �# � �7% 3AM� SRR62400692017-10-31A<�} A��8 AJ�`� SRX3347391AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���yO ! ! ! ! U �# � �7% 3AM� SRR62400552017-10-31AE�� A��� AJ�g� SRX3347405AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���xO ! ! ! ! U �# � �7% 3AM� SRR62400252017-10-31A<Z� A�� AJ�v� SRX3347435AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���{O ! ! ! ! U �# � �7% 3AM� SRR62400232017-10-31A5� A��0 AJ�w� SRX3347437AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���zO ! ! ! ! U �# � �7% 3AM� SRR62400152017-10-31A4� A�Щ@ AJ�{� SRX3347445AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���}O ! ! ! ! U �# � �7% 3AM� SRR62400382017-10-31A=fp A�tҀ AJ�p SRX3347422AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���|O ! ! ! ! U �# � �7% 3AM� SRR62400432017-10-31A>'! A��;� AJ�m� SRX3347417AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62400672017-10-31A9dx A�'N� AJ�a� SRX3347393AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���~O ! ! ! ! U �# � �7% 3AM� SRR62400412017-10-31A;p/ A�J�� AJ�n� SRX3347419AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62400272017-10-31A3�g A���P AJ�u� SRX3347433AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g��� O ! ! ! ! U �# � �7% 3AM� SRR62400572017-10-31A6� A�8�� AJ�f� SRX3347403AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62400482017-10-31A=>E A�\�� AJ�k SRX3347412AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62400202017-10-31ADg* A�:�� AJ�y SRX3347440AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62400242017-10-31A9o A�3� AJ�w SRX3347436AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62400442017-10-31A=�� A��6x AJ�m SRX3347416AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62400362017-10-31A9�� A�ʏ` AJ�q SRX3347424AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62400392017-10-31AB�� A�6�@ AJ�o� SRX3347421AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11�g���
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���HO ! ! ! ! U �# � �7% 3AM�� SRR62402532017-11-01A"�� A��x AJ��� SRX3347573AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g��� O ! ! ! ! U �# � �7% 3AM� SRR62400632017-10-31AE�A� A��M� AJ�c� SRX3347397AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�j SRA6268212018-05-10 18:11:11
& �& �g���JO ! ! ! ! U �# � �7% 3AM�Ӏ SRR62402562017-11-01A:I A�6�� AJ�� SRX3347570AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���IO ! ! ! ! U �# � �7% 3AM�� SRR62402592017-11-01A5� A��"p AJ��� SRX3347567AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���LO ! ! ! ! U �# � �7% 3AM�� SRR62402232017-11-01A@w� A��^� AJ��� SRX3347603AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���KO ! ! ! ! U �# � �7% 3AM�׀ SRR62402642017-11-01A>�� A�d;( AJ�� SRX3347562AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���NO ! ! ! ! U �# � �7% 3AM� SRR62402022017-11-01A;Ջ A��ʈ AJ�� SRX3347624AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���MO ! ! ! ! U �# � �7% 3AM�� SRR62402352017-11-01AH;q A�Ɩ0 AJ��� SRX3347591AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���PO ! ! ! ! U �# � �7% 3AM�ˀ SRR62402402017-11-01A$�� A�a?� AJ�� SRX3347586AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���OO ! ! ! ! U �# � �7% 3AM�Ԁ SRR62402582017-11-01A8B A��>` AJ�� SRX3347568AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���RO ! ! ! ! U �# � �7% 3AM� SRR62402162017-11-01A;k� A�H( AJ�� SRX3347610AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���QO ! ! ! ! U �# � �7% 3AM�� SRR62402572017-11-01A1�, A�J�@ AJ��� SRX3347569AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���TO ! ! ! ! U �# � �7% 3AM� SRR62402072017-11-01A89* A���� AJ��� SRX3347619AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���SO ! ! ! ! U �# � �7% 3AM�� SRR62402432017-11-01AHb � A�� AJ��� SRX3347583AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���VO ! ! ! ! U �# � �7% 3AM� SRR62402192017-11-01AC�ր A���� AJ��� SRX3347607AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���UO ! ! ! ! U �# � �7% 3AM�̀ SRR62402442017-11-01AJ�� A��( AJ�� SRX3347582AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���XO ! ! ! ! U �# � �7% 3AM� SRR62402132017-11-01A>�! A�\˘ AJ��� SRX3347613AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���WO ! ! ! ! U �# � �7% 3AM� SRR62401912017-11-01A:� A��� AJ��� SRX3347635AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���ZO ! ! ! ! U �# � �7% 3AM�� SRR62402512017-11-01A=�� A��"� AJ��� SRX3347575AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���YO ! ! ! ! U �# � �7% 3AM� SRR62401962017-11-01A:� A��0� AJ�� SRX3347630AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���\O ! ! ! ! U �# � �7% 3AM�Ȁ SRR62402342017-11-01AJr� A��� AJ�� SRX3347592AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���[O ! ! ! ! U �# � �7% 3AM� SRR62401902017-11-01A@�� A��� AJ�� SRX3347636AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���^O ! ! ! ! U �# � �7% 3AM�� SRR62402392017-11-01AFd A��РAJ��� SRX3347587AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���]O ! ! ! ! U �# � �7% 3AM�� SRR62402552017-11-01ABF A�gs AJ��� SRX3347571AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���`O ! ! ! ! U �# � �7% 3AM� SRR62401892017-11-01A2�N A�,�� AJ��� SRX3347637AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���_O ! ! ! ! U �# � �7% 3AM� SRR62402152017-11-01AD�� A���� AJ��� SRX3347611AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���bO ! ! ! ! U �# � �7% 3AM�� SRR62402672017-11-01A9Ď A��h� AJ��� SRX3347559AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���aO ! ! ! ! U �# � �7% 3AM� SRR62402202017-11-01AE? A�:� AJ�� SRX3347606AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���dO ! ! ! ! U �# � �7% 3AM� SRR62402002017-11-01A>"� A���� AJ�� SRX3347626AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���cO ! ! ! ! U �# � �7% 3AM� SRR62402112017-11-01A@�( A�� � AJ��� SRX3347615AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���fO ! ! ! ! U �# � �7% 3AM�Հ SRR62402602017-11-01A=�[ A��� AJ�� SRX3347566AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���eO ! ! ! ! U �# � �7% 3AM�ʀ SRR62402382017-11-01AE� A��܀ AJ�� SRX3347588AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���hO ! ! ! ! U �# � �7% 3AM�� SRR62402692017-11-01A<�U A�,Rx AJ�� SRX3347557AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���gO ! ! ! ! U �# � �7% 3AM� SRR62402032017-11-01A5�� A��8� AJ��� SRX3347623AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���jO ! ! ! ! U �# � �7% 3AM�� SRR62402252017-11-01AF1� A�Z�� AJ��� SRX3347601AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���iO ! ! ! ! U �# � �7% 3AM� SRR62401842017-11-01A6h� A���p AJ�� SRX3347642AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���lO ! ! ! ! U �# � �7% 3AM�� SRR62402332017-11-01A5r� A�x�� AJ��� SRX3347593AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���kO ! ! ! ! U �# � �7% 3AM� SRR62402052017-11-01A@�� A���P AJ��� SRX3347621AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���nO ! ! ! ! U �# � �7% 3AM� SRR62401812017-11-01A<�� A��@� AJ��� SRX3347645AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���mO ! ! ! ! U �# � �7% 3AM�ɀ SRR62402362017-11-01ACR� A��W AJ�� SRX3347590AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���pO ! ! ! ! U �# � �7% 3AM� SRR62401852017-11-01A5�� A���` AJ��� SRX3347641AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���oO ! ! ! ! U �# � �7% 3AM� SRR62402172017-11-01AD� A��Q� AJ��� SRX3347609AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���rO ! ! ! ! U �# � �7% 3AM� SRR62401922017-11-01A=�� A���� AJ�� SRX3347634AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���qO ! ! ! ! U �# � �7% 3AM�ڀ SRR62402702017-11-01AB�/ A�4�� AJ� SRX3347556AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���tO ! ! ! ! U �# � �7% 3AM�ŀ SRR62402282017-11-01A0U� A�eѠ AJ�� SRX3347598AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���sO ! ! ! ! U �# � �7% 3AM� SRR62401832017-11-01A4-� A��&� AJ��� SRX3347643AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���vO ! ! ! ! U �# � �7% 3AM� SRR62401982017-11-01A0�j A�$�� AJ�� SRX3347628AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���uO ! ! ! ! U �# � �7% 3AM� SRR62402662017-11-01A8�� A��� AJ�� SRX3347560AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���xO ! ! ! ! U �# � �7% 3AM� SRR62402042017-11-01A;� A��T� AJ�� SRX3347622AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���wO ! ! ! ! U �# � �7% 3AM�ۀ SRR62402722017-11-01AC� A��#� AJ�~ SRX3347554AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���zO ! ! ! ! U �# � �7% 3AM�̀ SRR62402422017-11-01A@}Y A��ٰ AJ�� SRX3347584AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���yO ! ! ! ! U �# � �7% 3AM�ր SRR62402622017-11-01A6t� A���� AJ�� SRX3347564AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���|O ! ! ! ! U �# � �7% 3AM�ƀ SRR62402302017-11-01A6D� A�q~ AJ�� SRX3347596AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���{O ! ! ! ! U �# � �7% 3AM�р SRR62402522017-11-01A2,= A���p AJ�� SRX3347574AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���~O ! ! ! ! U �# � �7% 3AM� SRR62401952017-11-01A<� A�� AJ��� SRX3347631AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���}O ! ! ! ! U �# � �7% 3AM� SRR62402092017-11-01A@� A��p AJ��� SRX3347617AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g��� O ! ! ! ! U �# � �7% 3AM�� SRR62402732017-11-01A?v� A���p AJ�}� SRX3347553AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62401992017-11-01A8�e A�*G� AJ��� SRX3347627AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM�� SRR62402212017-11-01A?< A�vc� AJ��� SRX3347605AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM�� SRR62402372017-11-01AIe1� A�(*� AJ��� SRX3347589AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM�� SRR62402312017-11-01AH�u� A�Jk� AJ��� SRX3347595AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62402182017-11-01AIK � A� 1� AJ�� SRX3347608AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62402122017-11-01AB��� A���( AJ�� SRX3347614AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM�� SRR62402632017-11-01ACI� A��� AJ��� SRX3347563AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM�� SRR62402472017-11-01A::� A�%� AJ��� SRX3347579AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM�π SRR62402482017-11-01A=� A��� AJ�� SRX3347578AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g��� O ! ! ! ! U �# � �7% 3AM�� SRR62402612017-11-01A9�? A�oz� AJ��� SRX3347565AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g��� O ! ! ! ! U �# � �7% 3AM�� SRR62402652017-11-01A8t A� �� AJ��� SRX3347561AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g��� O ! ! ! ! U �# � �7% 3AM�À SRR62402242017-11-01AB� A�`� AJ�� SRX3347602AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62402102017-11-01AKZ� A�=�@ AJ�� SRX3347616AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM�Ā SRR62402262017-11-01A;!� A� AJ�� SRX3347600AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM�� SRR62402272017-11-01A6�� A�0� AJ��� SRX3347599AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM�� SRR62402412017-11-01ABz�� A��� AJ��� SRX3347585AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM�� SRR62402492017-11-01AH��� A��� AJ��� SRX3347577AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62401872017-11-01A4'_ A��� AJ��� SRX3347639AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62401802017-11-01A8�' A�G�P AJ�� SRX3347646AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62402222017-11-01AA.� A�gA� AJ�� SRX3347604AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM�Ѐ SRR62402502017-11-01A8s� A� >� AJ�� SRX3347576AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM� SRR62402082017-11-01A=� A�ͤ� AJ�� SRX3347618AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62401972017-11-01A8� A�A�� AJ��� SRX3347629AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g���O ! ! ! ! U �# � �7% 3AM�� SRR62402712017-11-01ADC]� A�� AJ�~� SRX3347555AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62401932017-11-01A);� A���� AJ��� SRX3347633AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g��� O ! ! ! ! U �# � �7% 3AM� SRR62401882017-11-01A:-� A�=p AJ�� SRX3347638AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���O ! ! ! ! U �# � �7% 3AM� SRR62401862017-11-01A/�� A��� AJ�� SRX3347640AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g��� O ! ! ! ! U �# � �7% 3AM�Ҁ SRR62402542017-11-01A@ ( A�
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g��� O ! ! ! ! U �# � �7% 3AM� SRR62401822017-11-01A8U/ A��'� AJ�� SRX3347644AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
& �& �g��� O ! ! ! ! U �# � �7% 3AM�ـ SRR62402682017-11-01A>� A�"�� AJ�� SRX3347558AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g��� O ! ! ! ! U �# � �7% 3AM� SRR62402062017-11-01A9?G A��$P AJ�� SRX3347620AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���!O ! ! ! ! U �# � �7% 3AM� SRR62402142017-11-01AK�Z� A�� � AJ�� SRX3347612AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11�g���#O ! ! ! ! U �# � �7% 3AM�� SRR62402292017-11-01A;` A�A � AJ��� SRX3347597AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
J �J �C���<N ! ! ! ! # � �7% 3AN SRR62698512017-11-09A��2~ B�3` AJ�� SRX3375957AG�7� SRS2646464@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�g���%O ! ! ! ! U �# � �7% 3AM� SRR62402012017-11-01A<�� A���� AJ��� SRX3347625AFi
P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�l SRA6268282018-05-10 18:11:11
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�n �C���>N ! ! ! ! # � �7% 3AN � SRR62698522017-11-08A� :� B=,p AJ�À SRX3375956AGй SRS2646201@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���=N ! ! ! ! # � �7% 3AN ( SRR62698732017-11-08A��vt B�(T AJڹ SRX3375935AGй SRS2646201@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
4 }4 �C���@N ! ! ! ! # � �7% 3AN SRR62698552017-11-08A��o� B[/nL AJ�� SRX3375953AG�x� SRS2645247@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�}���?O ! ! ! ! U �-# � �7% 3AN ' SRR62698712017-11-09A� d B\b` AJں SRX3375937AF�W� P10SRS2428598%�synchronous ductal carcinoma in situisolate: P10 || age: 48 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: Tissue, Bulk DNA and single cell || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
J �J �C���BN ! ! ! ! # � �7% 3AN !� SRR62698602017-11-09A���� B#�`� AJھ SRX3375945AGѤ� SRS2646847@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�g���AO ! ! ! ! U �# � �7% 3AN * SRR62698772017-11-08A�$ B
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���CN ! ! ! ! # � �7% 3AN # SRR62698632017-11-08A�� � B
.^�@ AJڿ SRX3375947AG�� SRS2490581@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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�4 �}���FO ! ! ! ! U �-# � �7% 3AN ! SRR62698592017-11-09A��d B&C0� AJ�� SRX3375950AF�W� P10SRS2428598%�synchronous ductal carcinoma in situisolate: P10 || age: 48 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: Tissue, Bulk DNA and single cell || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���EN ! ! ! ! # � �7% 3AN ) SRR62698752017-11-08A�a� B��d@ AJڸ SRX3375933AG�� SRS2490581@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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P8SRS2496969%�synchronous ductal carcinoma in situisolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���GN ! ! ! ! # � �7% 3AN *� SRR62698782017-11-09A��M( B9�\� AJڶ� SRX3375930AG�x� SRS2645247@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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LXtp AJ�� SRX3375952AFV�� P5SRS2493573%�synchronous ductal carcinoma in situisolate: P5 || age: 47 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���IN ! ! ! ! # � �7% 3AN (� SRR62698742017-11-08A��� Bx<� AJڸ� SRX3375934AG�7� SRS2646464@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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�n �C���LN ! ! ! ! # � �7% 3AN '� SRR62698722017-11-09A�ڊ B �<Rp AJڹ� SRX3375936AGѤ� SRS2646847@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���KN ! ! ! ! # � �7% 3AN & SRR62698692017-11-09A�g^� B W�� AJڻ SRX3375939AGѤ� SRS2646847@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
J �J �C���NN ! ! ! ! # � �7% 3AN %� SRR62698682017-11-08A���� B*�* AJڻ� SRX3375940AG�� SRS2641973@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�g���MO ! ! ! ! U �# � �7% 3AN % SRR62698672017-11-08A��, B m�� AJڼ SRX3375941AFV�� P5SRS2493573%�synchronous ductal carcinoma in situisolate: P5 || age: 47 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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�� �&���PO ! ! ! ! �I# � �7% 3AN #� SRR62698642017-11-09A�S> B��� AJڽ� SRX3375944AF�! P1SRS2535762%�isolate: P1 || age: 57 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIB || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���ON ! ! ! ! # � �7% 3AN $ SRR62698652017-11-08A�L�4 B ��x AJڽ SRX3375943AG�x� SRS2645247@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
} �g���RO ! ! ! ! U �# � �7% 3AN +� SRR62698802017-11-08A�9�0 B Z~uH AJڵ� SRX3375928AFV�� P5SRS2493573%�synchronous ductal carcinoma in situisolate: P5 || age: 47 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�}���QO ! ! ! ! U �-# � �7% 3AN &� SRR62698702017-11-08A��@ B= " AJں� SRX3375938AF�W� P10SRS2428598%�synchronous ductal carcinoma in situisolate: P10 || age: 48 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: Tissue, Bulk DNA and single cell || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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ks6� AJ� SRX3375949AG�7� SRS2646464@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���TN ! ! ! ! # � �7% 3AN � SRR62698542017-11-09A��� BDɽ� AJ� SRX3375954AG�� SRS2490581@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���SN ! ! ! ! # � �7% 3AN + SRR62698792017-11-08A�U�( B�0� AJڶ SRX3375929AG�� SRS2641973@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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�� �&���WO ! ! ! ! �I# � �7% 3AN )� SRR62698762017-11-08A�~8 B�q�� AJڷ� SRX3375932AF�! P1SRS2535762%�isolate: P1 || age: 57 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIB || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11�C���VN ! ! ! ! # � �7% 3AN "� SRR62698622017-11-08A�� B
�#X AJڿ� SRX3375948AGй SRS2646201@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
M ��l M ����wN ! ! ! '! �# '�%% 3AN`�� SRR63120572017-11-22@�� @�� AK- SRX3412311ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����vN ! ! ! '! �# '�%% 3AN`� SRR63120602017-11-22@�M� Af��@ AK-� SRX3412308ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11�C���YN ! ! ! ! # � �7% 3AN � SRR62698582017-11-09A��� B�
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� B`z� AJ�� SRX3375955AF�! P1SRS2535762%�isolate: P1 || age: 57 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIB || BioSampleModel: Human@�� PRJNA397565SRP116771Synchronous ductal carcinoma in situ single cell DNA sequencingOtherDuctal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.Homo sapiensA'�6 SRA6295742018-05-10 18:11:11
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� � ��eF' ����~N ! ! ! '! �# '�%% 3AN`�� SRR63120552017-11-22@�Y� A`�7 AK- SRX3412313ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����}N ! ! ! '! �# '�%% 3AN`� SRR63120492017-11-22@� @ AL��� AK- SRX3412319ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����|N ! ! ! '! �# '�%% 3AN`� SRR63120502017-11-22@�� AU�&� AK-� SRX3412318ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����{N ! ! ! '! �# '�%% 3AN`�� SRR63120532017-11-22@�J` AWl�@ AK- SRX3412315ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����zN ! ! ! '! �# '�%% 3AN`� SRR63120482017-11-22@�>� AZ�z AK-� SRX3412320ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����yN ! ! ! '! �# '�%% 3AN`� SRR63120522017-11-22@�͠ As/�p AK-� SRX3412316ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����xN ! ! ! '! �# '�%% 3AN`� SRR63120562017-11-22@�m AT�� AK-� SRX3412312ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11
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� � ��e� � ���nN ! ! ! ! # �-�;E 3AN�~� SRR63139222017-11-24Ax㴐 A���� AKV� SRX3413862AH(V� SRS2707044@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11����N ! ! ! '! �# '�%% 3AN`� SRR63120472017-11-22@�� AD��� AK- SRX3412321ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����N ! ! ! '! �# '�%% 3AN`�� SRR63120592017-11-22@� A`�6` AK- SRX3412309ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����N ! ! ! '! �# '�%% 3AN`�� SRR63120512017-11-22@�P Ah�� AK- SRX3412317ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11���� N ! ! ! '! �# '�%% 3AN`� SRR63120582017-11-22@�l A(� AK-� SRX3412310ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11����N ! ! ! '! �# '�%% 3AN`� SRR63120542017-11-22@�X A]�� AK-� SRX3412314ADN Vaginal swabsSRS2246411%�isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human@��p PRJNA388787SRP108425Co2 Laser GSMOtherFractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspectsHomo sapiensA'�� SRA6326512018-05-10 18:11:11
x ^�x � ���rN ! ! ! ! # �-�;E 3ANb� SRR63139252017-11-22Aw �� A�� AK.� SRX3413859AH(W� SRS2707058@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11� ���qN ! ! ! ! # �-�;E 3AN�~ SRR63139212017-11-24Aw6� A�F%L� AKV�� SRX3413863AH(W SRS2707045@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11� ���pN ! ! ! ! # �-�;E 3ANb�� SRR63139272017-11-22A}T^� A� �n AK.ˀ SRX3413857AH(T� SRS2707040@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11� ���oN ! ! ! ! # �-�;E 3ANb� SRR63139292017-11-22A~��P A�t�` AK.� SRX3413855AH(S� SRS2707038@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11
x ^�x � ���vN ! ! ! ! # �-�;E 3AN�� SRR63139282017-11-24A}�B A�� AKV� SRX3413856AH(T SRS2707039@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11� ���uN ! ! ! ! # �-�;E 3ANb� SRR63139232017-11-22Ay�P A�� AK.� SRX3413861AH(V SRS2707043@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11� ���tN ! ! ! ! # �-�;E 3ANb�� SRR63139242017-11-22Av�� A�G�` AK.̀ SRX3413860AH(U� SRS2707042@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11� ���sN ! ! ! ! # �-�;E 3AN� SRR63139262017-11-24Aw�v� A� � AKV�� SRX3413858AH(U SRS2707041@��� PRJNA358389SRP095725Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinomaExome SequencingWe designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.Mus musculus strain:C57BL/6NA'�| SRA6329562018-05-10 18:11:11
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h� ����?N ! ! ! ! �;�I 3AQ�4 SRR69207442018-03-30A� � B$Պ� AO� SRX3868137AK(: SRS3042210@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11����>N ! ! ! ! �;�I 3AQ�4� SRR69207462018-03-30A��d< B"7� d AO� SRX3868135AK(; SRS3042212@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11
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h� ����AN ! ! ! ! �;�I 3AQ�4@ SRR69207452018-03-30A�kK� B$��� AO� SRX3868136AK(<� SRS3042215@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11����@N ! ! ! ! �;�I 3AQ�2� SRR69207392018-03-30A���� B#�l�` AO� SRX3868142AK(9� SRS3042208@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11
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h� ����CN ! ! ! ! �;�I 3AQ�3@ SRR69207412018-03-30A��� B&" @ AO� SRX3868140AK(= SRS3042216@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11����BN ! ! ! ! �;�I 3AQ�3� SRR69207422018-03-30AQfl� AԆ�J� AO� SRX3868139AK(:� SRS3042211@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11
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h� ����EN ! ! ! ! �;�I 3AQ�3� SRR69207432018-03-30A��h B (L� AO� SRX3868138AK(;� SRS3042213@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11����DN ! ! ! ! �;�I 3AQ�2� SRR69207382018-03-30A�M6 B#:�� AO� SRX3868143AK(< SRS3042214@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11
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h� ����GN ! ! ! ! �;�I 3AQ�5 SRR69207482018-03-30A�VdD B#E�H8 AO� SRX3868133AK(8� SRS3042207@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11����FN ! ! ! ! �;�I 3AQ�3 SRR69207402018-03-30A�Px B �t�� AO� SRX3868141AK(9 SRS3042209@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11
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h ����HN ! ! ! ! �;�I 3AQ�4� SRR69207472018-03-30A���� B!�9� AO� SRX3868134AK(8 SRS3042206@ݺ� 145181SRP015682Poecilia formosa strain:female Genome sequencing and assemblyWhole Genome SequencingThe Amazon Molly, Poecilia formosa, was first introduced to biomedical research in 1979 when it was listed in the "Registry of Animal Models for Human Disease" for DNA damage studies. Since then it has been used for carcinogenicity studies with physical and chemical agents, as test organism in ecotoxicology, for research on infectious diseases, and for experimental cancer research. This fish stands out from all other aquatic models by the unique feature of genetic clonality. This is due to its unusual mode of reproduction. Females produce diploid eggs without meiosis, which are then triggered for parthenogenetic development by sperm of males from related species. There is, however, no paternal genetic contribution and all offspring develop as clones of their maternal lineage. The proven true clonality thus allows researchers to perform experiments with animals that are genetically identical. This guarantees the utmost reproducibility of independent studies, a stereotype development of diseases or physiological processes under scrutiny and a highly comparable biological material.Poecilia formosa strain:femaleA)�� SRA6777922018-05-10 18:11:11 e +6C +6C +6C +6C +6C +6C +6C +6C +6C +6C +6C +6C ω +6C +6C +6C +6C +6C �� "
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3!studyentrez_linktextNCBI controlled vocabulary of permitted cross references. Please see http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? .2011-10-28 18:15:41P S
3 studyurl_linktextText label to display for the link.2011-10-28 18:15:41-
3 studyena_linktext2011-10-28 18:15:41.
3 studyddbj_linktext2011-10-28 18:15:410 #
3 studyentrez_linktext2011-10-28 18:15:41.
3 studyxref_linktext2011-10-28 18:15:41-
3studysra_linktext2011-10-28 18:15:41� #�C
3studybroker_namevarcharBroker authority of this document. If not provided, then the broker is considered "direct".2011-10-28 18:15:41� '�Q3studyprimary_studyvarcharWhether this study object is designated as the primary source of the study or project information.yes, no2011-10-28 18:15:41�c +�i
3studyrelated_studiestextRelated study or project record from a list of supported databases. The study's information is derived from this project record rather than stored as first class information.2011-10-28 18:15:41h/q
3studystudy_descriptiontextMore extensive free-form description of the study.2011-10-28 18:15:41�5 3�
3studycenter_project_namevarcharSubmitter defined project name. This field is intended for backward tracking of the study record to the submitter's LIMS.2011-10-28 18:15:41�? )�#
3studystudy_abstracttextBriefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.2011-10-28 18:15:41�
!�M� 3studystudy_typevarcharThe STUDY_TYPE presents a controlled vocabulary for expressing the overall purpose of the study.Whole Genome Sequencing, Exome Sequencing, Resequencing, Cancer Genomics, Population Genomics, Pooled Clone Sequencing, Metagenomics, Epigenetics, Transcriptome Analysis, RNASeq, Gene Regulation Study, Synthetic Genomics, Forensic or Paleo-genomics, Other2011-10-28 18:15:41h#w
3studystudy_titlevarcharTitle of the study as would be used in a publication.2011-10-28 18:15:41j
3studyaccessionvarcharThe document's accession as assigned by the Home Archive.2011-10-28 18:15:41�0 �
3studyaliasvarcharSubmitter designated name of the SRA document of this type. At minimum alias should be unique throughout the submission of this document type. If center_name is specified, the name should be unique in all submissions from that center of this document type.2011-10-28 18:15:41&
3studyIDint2011-10-28 18:15:41q!% y
3submissiondate_updatedtimestampDatetime the record synchronized with SRA, ERA and DRA2011-10-28 18:15:41x !+�
3submissionsubmission_datedateSubmitter assigned preparation date of this submission object.2011-10-28 18:15:41c
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3
submissionlab_namevarcharLaboratory name within submitting institution.2011-10-28 18:15:412 !
3 submissionena_linktext2011-10-28 18:15:413 !
3 submissionddbj_linktext2011-10-28 18:15:415
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3
submissionentrez_linktext2011-10-28 18:15:413 !
3 submissionxref_linktext2011-10-28 18:15:412!
3submissionsra_linktext2011-10-28 18:15:41� !#�C
3submissionbroker_namevarcharBroker authority of this document. If not provided, then the broker is considered "direct".2011-10-28 18:15:41Q!#?
3submissioncenter_namevarcharCenter name of submitter.2011-10-28 18:15:41P!O
3submissionfilestextFiles included in the submission.2011-10-28 18:15:41W!1C
3submissionsubmission_commenttextSubmitter assigned comment.2011-10-28 18:15:41�Y !�Y
3submissionaliasvarcharSbmitter supplied name or id for the submission. This value can be used by the submitterto track a submission without waiting for the Archive to assign an accession.2011-10-28 18:15:41o!
3submissionaccessionvarcharThe document's accession as assigned by the Home Archive.2011-10-28 18:15:41* !
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3!studyentrez_linktextNCBI controlled vocabulary of permitted cross references. Please see http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? .2011-10-28 18:15:41P S
3 studyurl_linktextText label to display for the link.2011-10-28 18:15:41-
3 studyena_linktext2011-10-28 18:15:41.
3 studyddbj_linktext2011-10-28 18:15:410 #
3 studyentrez_linktext2011-10-28 18:15:41.
3 studyxref_linktext2011-10-28 18:15:41-
3studysra_linktext2011-10-28 18:15:41� #�C
3studybroker_namevarcharBroker authority of this document. If not provided, then the broker is considered "direct".2011-10-28 18:15:41� '�Q3studyprimary_studyvarcharWhether this study object is designated as the primary source of the study or project information.yes, no2011-10-28 18:15:41�c +�i
3studyrelated_studiestextRelated study or project record from a list of supported databases. The study's information is derived from this project record rather than stored as first class information.2011-10-28 18:15:41h/q
3studystudy_descriptiontextMore extensive free-form description of the study.2011-10-28 18:15:41�5 3�
3studycenter_project_namevarcharSubmitter defined project name. This field is intended for backward tracking of the study record to the submitter's LIMS.2011-10-28 18:15:41�? )�#
3studystudy_abstracttextBriefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.2011-10-28 18:15:41�
!�M� 3studystudy_typevarcharThe STUDY_TYPE presents a controlled vocabulary for expressing the overall purpose of the study.Whole Genome Sequencing, Exome Sequencing, Resequencing, Cancer Genomics, Population Genomics, Pooled Clone Sequencing, Metagenomics, Epigenetics, Transcriptome Analysis, RNASeq, Gene Regulation Study, Synthetic Genomics, Forensic or Paleo-genomics, Other2011-10-28 18:15:41h#w
3studystudy_titlevarcharTitle of the study as would be used in a publication.2011-10-28 18:15:41j
3studyaccessionvarcharThe document's accession as assigned by the Home Archive.2011-10-28 18:15:41�0 �
3studyaliasvarcharSubmitter designated name of the SRA document of this type. At minimum alias should be unique throughout the submission of this document type. If center_name is specified, the name should be unique in all submissions from that center of this document type.2011-10-28 18:15:41&
3studyIDint2011-10-28 18:15:41q!% y
3submissiondate_updatedtimestampDatetime the record synchronized with SRA, ERA and DRA2011-10-28 18:15:41x !+�
3submissionsubmission_datedateSubmitter assigned preparation date of this submission object.2011-10-28 18:15:41c
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submissionlab_namevarcharLaboratory name within submitting institution.2011-10-28 18:15:412 !
3 submissionena_linktext2011-10-28 18:15:413 !
3 submissionddbj_linktext2011-10-28 18:15:415
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3
submissionentrez_linktext2011-10-28 18:15:413 !
3 submissionxref_linktext2011-10-28 18:15:412!
3submissionsra_linktext2011-10-28 18:15:41� !#�C
3submissionbroker_namevarcharBroker authority of this document. If not provided, then the broker is considered "direct".2011-10-28 18:15:41Q!#?
3submissioncenter_namevarcharCenter name of submitter.2011-10-28 18:15:41P!O
3submissionfilestextFiles included in the submission.2011-10-28 18:15:41W!1C
3submissionsubmission_commenttextSubmitter assigned comment.2011-10-28 18:15:41�Y !�Y
3submissionaliasvarcharSbmitter supplied name or id for the submission. This value can be used by the submitterto track a submission without waiting for the Archive to assign an accession.2011-10-28 18:15:41o!
3submissionaccessionvarcharThe document's accession as assigned by the Home Archive.2011-10-28 18:15:41* !
3submissionIDint2011-10-28 18:15:41
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3>experimentcenter_namevarcharOwner authority of this document and namespace for submitter's name of this document. If not provided, then the submitter is regarded as 'Individual' and document resolution can only happen within the submission.2011-10-28 18:15:41o=!
3=experimentaccessionvarcharThe document's accession as assigned by the Home Archive.2011-10-28 18:15:41�3< !�
3<experimentaliasvarcharSubmitter designated name of the SRA document of this type. At minimum alias should be unique throughout the submission of this document type. If center_name is specified, the name should be unique in all submissions from that center of this document type.2011-10-28 18:15:41F;! /
3;experimentfastqFTPvarcharftp to fastq file2011-10-28 18:15:41U:!O
3:experimentbamFilevarcharAvailable converted bam file name2011-10-28 18:15:41+9!
39experimentIDint2011-10-28 18:15:41m8% y
38sampledate_updatedtimestampDatetime the record synchronized with SRA, ERA and DRA2011-10-28 18:15:41.7
37sampleena_linktext2011-10-28 18:15:41/6
36sampleddbj_linktext2011-10-28 18:15:4115#
35sampleentrez_linktext2011-10-28 18:15:41/4
34samplexref_linktext2011-10-28 18:15:41.3
33samplesra_linktext2011-10-28 18:15:41�2 #�C
32samplebroker_namevarcharBroker authority of this document. If not provided, then the broker is considered "direct".2011-10-28 18:15:41Q155
31samplesubmission_accessionvarcharSubmission accession2011-10-28 18:15:41�0 -�#
30samplesample_attributetextProperties and attributes of a sample. These can be entered as free-form tag-value pairs. For certain studies, submitters may be asked to follow a community established ontology when describing the work.2011-10-28 18:15:41�./ #�
3/sampleentrez_linktextNCBI controlled vocabulary of permitted cross references. Please see http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? .2011-10-28 18:15:41Q. S
3.sampleurl_linktextText label to display for the link.2011-10-28 18:15:41� - #�)
3-sampledescriptiontextFree-form text describing the sample, its origin, and its method of isolation.2011-10-28 18:15:41� , +�-
3,sampleindividual_namevarcharIndividual name of the sample. This field can be used to identify the individual identity of a sample where appropriate (this is usually NOT appropriate for human subjects). Example: "Glennie" the platypus.2011-10-28 18:15:41�+ +�
3+samplescientific_namevarcharScientific name of sample that distinguishes its taxonomy. Please use a name or synonym that is tracked in the INSDC Taxonomy database. Also, this field can be used to confirm the TAXON_ID setting.2011-10-28 18:15:41�* +�+
3*sampleanonymized_namevarcharAnonymous public name of the sample. For example, HapMap human isolate NA12878.2011-10-28 18:15:41q) #�
3)samplecommon_namevarcharGenBank common name of the organism. Examples: human, mouse.2011-10-28 18:15:41�( �Y
3(sampletaxon_idintNCBI Taxonomy Identifier. This is appropriate for individual organisms and some environmental samples.2011-10-28 18:15:41k'
3'sampleaccessionvarcharThe document's accession as assigned by the Home Archive.2011-10-28 18:15:41�/& �
3&samplealiasvarcharSubmitter designated name of the SRA document of this type. At minimum alias should be unique throughout the submission of this document type. If center_name is specified, the name should be unique in all submissions from that center of this document type.2011-10-28 18:15:41'%
3%sampleIDint2011-10-28 18:15:41l$% y
3$studydate_updatedtimestampDatetime the record synchronized with SRA, ERA and DRA2011-10-28 18:15:41P#55
3#studysubmission_accessionvarcharSubmission accession2011-10-28 18:15:41�" +�%
3"studystudy_attributetextProperties and attributes of the study. These can be entered as free-form tag-value pairs. For certain studies, submitters may be asked to follow a community established ontology when describing the work.2011-10-28 18:15:41
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3Yexperimenturl_linktextThe internet service link (file:, http:, ftp:, etc).2011-10-28 18:15:41@X!)
3Xexperimentqtypevarcharphred or other2011-10-28 18:15:41BW!!#
3WexperimentmultipliervarcharDEPRECATED.2011-10-28 18:15:41�V !-�
3Vexperimentnumber_of_levelsintDEPRECATED. Number of distinct values possible with this scoring system.2011-10-28 18:15:41lU!)o
3Uexperimentquality_scorervarcharName and version of the quality scoring software.2011-10-28 18:15:41oT!#{
3Texperimentbase_callervarcharName and version of the base or color calling software.2011-10-28 18:15:41TS!)?
3Sexperimentsequence_spacevarcharBase Space or Color Space2011-10-28 18:15:41=R!3
3Rexperimentplatform_parameterstext2011-10-28 18:15:41�hQ !-M�!3Qexperimentinstrument_modelvarcharInstrument model for a platform.LS454: 454 GS, 454 GS 20, 454 GS FLX, 454 Titanium, GS 20, GS FLX, unspecified; ILLUMINA: Solexa 1G Genome Analyzer, Illumina Genome Analyzer, Illumina Genome Analyzer II, unspecified; ABI_SOLID: AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, unspecified2011-10-28 18:15:41� P
! ��3PexperimentplatformvarcharThe PLATFORM record selects which sequencing platform and platform-specific runtime parameters. This will be determined by the Center.LS454, ILLUMINA, HELICOS, ABI_SOLID, COMPLETE_GENOMICS, PACBIO_SMRT2011-10-28 18:15:41�O
! �7�3Oexperimentread_spectextContains READ_INDEX, READ_LABEL, READ_CLASS, READ_TYPE, BASE_COORD, RELATIVE_ORDER, CYCLE_COORD, EXPECTED_BASECALL, EXPECTED_BASECALL_TABLE, BASECALLREAD_TYPE: Forward, Reverse, Adapter, Primer, Linker, BarCode, Other2011-10-28 18:15:41�9N !%�
3Nexperimentadapter_specvarcharSome technologies will require knowledge of the sequencing adapter or the last base of the adapter in order to decode the spot.2011-10-28 18:15:414M!#
3Mexperimentspot_lengthint2011-10-28 18:15:41� L !G�;
3Lexperimentlibrary_construction_protocoltextFree form text describing the protocol by which the sequencing library was constructed.2011-10-28 18:15:41:K!'
3Kexperimenttargeted_locivarchar2011-10-28 18:15:41�
J !)� -3Jexperimentlibrary_layoutvarcharLIBRARY_LAYOUT specifies whether to expect single, paired, or other configuration of reads. In the case of paired reads, information about the relative distance and orientation is specified.SINGLE or PAIRED2011-10-28 18:15:41�0I
!/�/�K3Iexperimentlibrary_selectionvarcharWhether any method was used to select and/or enrich the material being sequenced.RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, CF-S, CF-M, CF-H, CF-T, MSLL, cDNA, ChIP, MNase, DNAse, Hybrid Selection, Reduced Representation, other, unspecified2011-10-28 18:15:41�>H !)�/o3Hexperimentlibrary_sourcevarcharThe LIBRARY_SOURCE specifies the type of source material that is being sequenced.GENOMIC, NON GENOMIC, SYNTHETIC, VIRAL RNA, OTHER2011-10-28 18:15:41�G !-k�Y3Gexperimentlibrary_strategyvarcharSequencing technique intended for this library.WGS,WCS,WXS,CLONE,CLONEEND,POOLCLONE,FINISHING,AMPLICON,RNA-Seq,EST,FL-cDNA,CTS,ChIP-Seq,MNase-Seq,Dase-Hypersensitivity,Bisulfite-Seq,MRE-Seq,MeDIP-Seq,MBD-Seq,Other2011-10-28 18:15:41_F!%Y
3Fexperimentlibrary_namevarcharThe submitter's name for this library.2011-10-28 18:15:417E!'
3Eexperimentsample_membertext2011-10-28 18:15:41ND!-/
3Dexperimentsample_accessionvarcharSample accession.2011-10-28 18:15:41DC!#%
3Cexperimentsample_namevarcharSample name.2011-10-28 18:15:41�B !1�?
3Bexperimentdesign_descriptiontextMore details about the setup and goals of the experiment as supplied by the Investigator.2011-10-28 18:15:41LA!+-
3Aexperimentstudy_accessionvarcharStudy accession.2011-10-28 18:15:41B@!!#
3@experimentstudy_namevarcharStudy name.2011-10-28 18:15:41�V? !�S
3?experimenttitlevarcharShort text that can be used to call out experiment records in searches or in displays. This element is technically optional but should be used for all new records.2011-10-28 18:15:41
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3}data_blocksectorintHigher level partition of run data to which this data block pertains. (454) not used (Illumina) Lane number (SOLiD) slide (Helicos) channel2011-10-28 18:15:41�4| !�
3|data_blocknamevarcharThe plate/slide/flowcell name for this data block. (454) plate name (Illumina) flowcell name (SOLiD) slide name (Helicos) flowcell2011-10-28 18:15:41+{!
3{data_blockIDint2011-10-28 18:15:41jz% y
3zrundate_updatedtimestampDatetime the record synchronized with SRA, ERA and DRA2011-10-28 18:15:41+y
3yrunena_linktext2011-10-28 18:15:41,x
3xrunddbj_linktext2011-10-28 18:15:41.w#
3wrunentrez_linktext2011-10-28 18:15:41,v
3vrunxref_linktext2011-10-28 18:15:41+u
3urunsra_linktext2011-10-28 18:15:41�
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3trunbroker_namevarcharBroker authority of this document. If not provided, then the broker is considered "direct".2011-10-28 18:15:41Ns55
3srunsubmission_accessionvarcharSubmission accession2011-10-28 18:15:41�yr '�
3rrunrun_attributetextProperties and attributes of a RUN. These can be entered as free-form tag-value pairs. For certain studies, submitters may be asked to follow a community established ontology when describing the work.2011-10-28 18:15:41�+q #�
3qrunentrez_linktextNCBI controlled vocabulary of permitted cross references. Please see http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? .2011-10-28 18:15:41_p u
3prunurl_linktextThe internet service link (file:, http:, ftp:, etc).2011-10-28 18:15:41Do++
3orunexperiment_namevarcharExperiment name2011-10-28 18:15:41Nn55
3nrunexperiment_accessionvarcharExperiment accession2011-10-28 18:15:41pm /�
3mruntotal_data_blocksintDEPRECATED. The number of data blocks to expect in this run.2011-10-28 18:15:41�l !�O
3lrunrun_centervarcharIf applicable, the name of the contract sequencing center that executed the run. Example: 454MSC.2011-10-28 18:15:41�k �Y
3krunrun_filetextDEPRECATED. Name of the submission file containing the run. This file may have included multiple runs.2011-10-28 18:15:41Lj O
3jrunrun_datedateISO date when the run took place.2011-10-28 18:15:41si +�
3iruninstrument_namevarcharCenter-assigned name or id of the instrument used in the run.2011-10-28 18:15:41hh
3hrunaccessionvarcharThe document's accession as assigned by the Home Archive.2011-10-28 18:15:41�,g �
3grunaliasvarcharSubmitter designated name of the SRA document of this type. At minimum alias should be unique throughout the submission of this document type. If center_name is specified, the name should be unique in all submissions from that center of this document type.2011-10-28 18:15:41?f /
3frunfastqFTPvarcharftp to fastq file2011-10-28 18:15:41NeO
3erunbamFilevarcharAvailable converted bam file name2011-10-28 18:15:41$d
3drunIDint2011-10-28 18:15:41qc!% y
3cexperimentdate_updatedtimestampDatetime the record synchronized with SRA, ERA and DRA2011-10-28 18:15:412b!
3bexperimentena_linktext2011-10-28 18:15:413a!
3aexperimentddbj_linktext2011-10-28 18:15:415`!#
3`experimententrez_linktext2011-10-28 18:15:413_!
3_experimentxref_linktext2011-10-28 18:15:412^!
3^experimentsra_linktext2011-10-28 18:15:41�] !#�C
3]experimentbroker_namevarcharBroker authority of this document. If not provided, then the broker is considered "direct".2011-10-28 18:15:41U\!55
3\experimentsubmission_accessionvarcharSubmission accession2011-10-28 18:15:41� [ !5�K
3[experimentexperiment_attributetextProperties and attributes of the experiment. These can be entered as free-form tag-value pairs.2011-10-28 18:15:41�2Z !#�
3Zexperimententrez_linktextNCBI controlled vocabulary of permitted cross references. Please see http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? .2011-10-28 18:15:41
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3 �data_blockdate_updatedtimestampDatetime the record synchronized with SRA, ERA and DRA2011-10-28 18:15:41O� !'5
3 �data_blockrun_accessionvarcharSubmission accession2011-10-28 18:15:41�Z
!�/�73data_blockfilesvarcharActual run data are contained in one of the files listed in the submission manifest. Each data block is represented by one SRF file, one SFF file, one compressed fastq file, or one compressed tar archive file.File Tpes: sra, srf, sff, fastq, tab, _seq.txt, _prb.txt, _sig2.txt, _qhg.txt, 454_native, 454_native_seq, 454_native_qual, Helicos_native, Illumina_native, Illumina_native_seq, Illumina_native_prb, Illumina_native_int, Illumina_native_qseq, Illumina_native_fastq, Illumina_native_scarf, SOLiD_native, SOLiD_native_csfasta, SOLiD_native_qual2011-10-28 18:15:41�q~ !�
3~data_blockregionintLower level partition of run data to which this data block pertains, typically the field of view for the imaging camera. (454) 0 if whole plate is used, 1..16 for gasket partition. (Illumina) Tile number (1..200+), or use 0 if file contains all tiles. (SOLiD) Panel number (1..4096), or use 0 if file contains all panels.2011-10-28 18:15:41 � N������zk\M?1#���������ugYK=/!
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