# submission

submission_alias: DRA002722
submission_accession: DRA002722
center_name: KYOTO_SC
sradb_updated: 2016-11-20 17:30:34
lab_name:
Laboratory of Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University


submission_accession: ERA008987
center_name: SC
sradb_updated: 2016-11-20 17:34:08
submission_alias:
Identification of the expression profile of Staphylococcus aureus grown in the presence or absence of a fatty acid. -sc-2010-06-07


submission_alias: SRA000241
submission_accession: SRA000241
center_name: WUGSC
lab_name: Genome Sequencing Center
submission_date: 2007-08-23
sradb_updated: 2016-11-20 21:16:10
submission_comment:
Ftp 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.


submission_alias: SRA000246
submission_accession: SRA000246
center_name: WUGSC
lab_name: Genome Sequencing Center
submission_date: 2007-10-25
sradb_updated: 2016-11-20 21:16:10
submission_comment:
Ftp 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.


# study

study_alias: DRP002820
study_accession: DRP002820
study_title: Transcriptome sequence of planarian Dugesia japonica
study_type: Other
center_name: KYOTO_SC
center_project_name: Dugesia japonica strain:GI
xref_link: pubmed: 26588467
submission_accession: DRA002722
sradb_updated: 2017-09-21 20:27:02
study_abstract:
Transcriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.

study_description:
Transcriptome sequence of asexual reproductive clonal planarian Dugesia japonica GI strain, which was derived from a single animal.


study_alias: DRP002612
study_accession: DRP002612
study_title: Bursaphelenchus xylophilus transcriptome
study_type: Other
center_name: MIYAZAKI
submission_accession: DRA002992
sradb_updated: 2016-11-20 16:43:24
study_abstract:
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.

study_description:
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.


study_alias: DRP002638
study_accession: DRP002638
study_title: RNAseq in a fully controlled plant factory
study_type: Transcriptome Analysis
center_name: OSAKA_PREF
center_project_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2017-09-21 20:27:47
study_abstract:
Transcriptome 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.

study_description:
Transcriptome 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.


study_accession: ERP000233
study_type: Transcriptome Analysis
study_abstract: Link to project web page.
center_name: SC
submission_accession: ERA008987
sradb_updated: 2016-11-20 16:43:49
study_alias:
Identification of the expression profile of Staphylococcus aureus grown in the presence or absence of a fatty acid. -sc-2010-06-07

study_title:
Identification of the expression profile of Staphylococcus aureus grown in the presence or absence of a fatty acid.

center_project_name:
Identification of the expression profile of Staphylococcus aureus grown in the presence or absence of a fatty acid.

study_description:
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/


study_alias: E-MTAB-387
study_accession: ERP000350
study_title: RNA sequencing in E. coli K12
study_type: Other
broker_name: ArrayExpress
center_name: EMBL_Heidelberg
center_project_name: RNA sequencing in E. coli K12
study_url_link: E-MTAB-387 in ArrayExpress: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MTAB-387
submission_accession: ERA014184
sradb_updated: 2016-11-20 16:43:52
study_description:
Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phase


study_alias: E-MTAB-861
study_accession: ERP001030
study_title: wheat starchy endosperm RNA-Seq
study_type: Other
broker_name: ArrayExpress
center_name: GATC Biotech AG
center_project_name: wheat starchy endosperm RNA-Seq
study_url_link: E-MTAB-861 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-861
submission_accession: ERA070843
sradb_updated: 2016-11-20 16:44:06
study_description:
Transcriptome 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.


study_alias: E-MTAB-1585
study_accession: ERP002405
study_title: Transcriptional profiling of 7SK knockdown in mouse embryonic stem cells
study_type: Other
broker_name: ArrayExpress
center_name: EMBL-EBI
center_project_name: Transcriptional profiling of 7SK knockdown in mouse embryonic stem cells
study_url_link: E-MTAB-1585 in ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585
submission_accession: ERA203799
sradb_updated: 2016-11-20 16:45:02
study_abstract:
Transcriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.

study_description:
Transcriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.


study_alias: 2140628333
study_accession: SRP000017
study_title: Reference genome for the Human Microbiome Project
study_type: Whole Genome Sequencing
center_name: WUGSC
center_project_name: Streptococcus infantarius subsp. infantarius ATCC BAA-102
study_url_link: GOLD: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi02364
study_attribute: parent_bioproject: PRJNA28331
submission_accession: SRA000246
sradb_updated: 2017-01-26 20:08:16
study_abstract:
<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.


study_alias: Melanoma_Transcriptome
study_accession: SRP000931
study_title: Melanoma Cell Transcriptome
study_type: Other
center_name: BI
center_project_name: Homo sapiens
xref_link: pubmed: 20179022
study_attribute: parent_bioproject: PRJNA118501
submission_accession: SRA009053
sradb_updated: 2017-09-21 20:38:11
study_abstract:
Paired 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.


study_alias: Trout transcriptome-454
study_accession: SRP001007
study_title: Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approaches
study_type: Other
center_name: West Virginia University,
center_project_name: Oncorhynchus mykiss
xref_link: pubmed: 20942956
submission_accession: SRA009276
sradb_updated: 2016-11-20 16:51:03
study_abstract:
Background: 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.


study_alias: PRJNA311339
study_accession: SRP116664
study_title: Transcriptome analysis of domesticated breadfruit and its wild relatives
study_type: Other
center_name: BioProject
center_project_name: Artocarpus
submission_accession: SRA604752
sradb_updated: 2017-09-07 20:02:00
study_abstract:
The 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.


study_alias: PRJNA399503
study_accession: SRP116668
study_type: Whole Genome Sequencing
center_name: BioProject
center_project_name: Homo sapiens
submission_accession: SRA604756
sradb_updated: 2017-09-07 20:02:00
study_title:
Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients

study_abstract:
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. 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.


study_alias: GSE104177
study_accession: SRP118776
study_title: Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenografts
study_type: Transcriptome Analysis
center_name: GEO
center_project_name: GSE104177
submission_accession: SRA612572
sradb_updated: 2017-10-12 21:29:04
study_abstract:
These 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 study


study_alias: GSE104193
study_accession: SRP118788
study_type: Transcriptome Analysis
center_name: GEO
center_project_name: GSE104193
submission_accession: SRA612618
sradb_updated: 2017-10-12 21:29:04
study_title:
Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ÃŸ signalling and malignant features in vitro and in vivoÂ 

study_abstract:
We 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 < â€“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 lines


study_alias: PRJNA412025
study_accession: SRP119112
study_type: Other
center_name: BioProject
center_project_name: Homo sapiens
study_url_link: TEX study: https://clinicaltrials.gov/ct2/show/NCT01433614
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:06:45
study_title:
Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)

study_abstract:
Exome 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)


study_alias: GSE104711
study_accession: SRP119540
study_title: K8 CLIP-Seq in KSHV reactivated BCBL-1 cells
study_type: Other
center_name: GEO
center_project_name: GSE104711
submission_accession: SRA617783
sradb_updated: 2017-10-12 21:29:13
study_abstract:
KSHV 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.


study_alias: GSE104714
study_accession: SRP119557
study_title: Clustering gene expression time series data using an infinite Gaussian process mixture model
study_type: Transcriptome Analysis
center_name: GEO
center_project_name: GSE104714
submission_accession: SRA617809
sradb_updated: 2017-10-12 21:29:13
study_abstract:
In 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.


study_alias: GSE104716
study_accession: SRP119575
study_title: RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretion
study_type: Transcriptome Analysis
center_name: GEO
center_project_name: GSE104716
submission_accession: SRA617842
sradb_updated: 2017-10-12 21:29:14
study_abstract:
We 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.


study_alias: GSE104725
study_accession: SRP119595
study_title: Quantitative Transcriptome Analysis of T cells stimulated with STING ligands
study_type: Transcriptome Analysis
center_name: GEO
center_project_name: GSE104725
submission_accession: SRA617887
sradb_updated: 2017-10-12 21:29:14
study_abstract:
STING 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: NaÃ¯ve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.


study_alias: GSE104734
study_accession: SRP119609
study_title: RNA-Seq Profiling of Pharmacological Activation of PXR and CAR Mice
study_type: Transcriptome Analysis
center_name: GEO
center_project_name: GSE104734
submission_accession: SRA617912
sradb_updated: 2017-10-12 21:29:14
study_abstract:
This 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.


study_alias: GSE104738
study_accession: SRP119613
study_type: Transcriptome Analysis
center_name: GEO
center_project_name: GSE104738
submission_accession: SRA617916
sradb_updated: 2017-10-12 21:29:14
study_title:
The compact genome in the clavulanic acid producing Streptomyces  strain unravels a variety of horizontal transfer reservoirs

study_abstract:
Bacterial 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 sequencing


# sample

sample_alias: DRS005661
sample_accession: DRS005661
center_name: NIVTS
scientific_name: Allium fistulosum
common_name: bunching onion
submission_accession: DRA000945
sradb_updated: 2016-11-20 05:19:02
description:
Mixture 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).


sample_alias: DRS021957
sample_accession: DRS021957
center_name: KYOTO_SC
scientific_name: Dugesia japonica
submission_accession: DRA002722
sradb_updated: 2016-11-20 05:21:26
sample_attribute:
sex: 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


sample_alias: DRS021958
sample_accession: DRS021958
center_name: KYOTO_SC
scientific_name: Dugesia japonica
submission_accession: DRA002722
sradb_updated: 2016-11-20 05:21:26
sample_attribute:
sex: 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


sample_alias: DRS021959
sample_accession: DRS021959
center_name: KYOTO_SC
scientific_name: Dugesia japonica
submission_accession: DRA002722
sradb_updated: 2016-11-20 05:21:26
sample_attribute:
sex: 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


sample_alias: DRS019417
sample_accession: DRS019417
center_name: MIYAZAKI
scientific_name: Bursaphelenchus xylophilus
submission_accession: DRA002992
sradb_updated: 2016-11-20 05:21:49
sample_attribute:
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


sample_alias: DRS019430
sample_accession: DRS019430
center_name: MIYAZAKI
scientific_name: Bursaphelenchus xylophilus
submission_accession: DRA002996
sradb_updated: 2016-11-20 05:21:49
sample_attribute:
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


sample_alias: DRS019563
sample_accession: DRS019563
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019564
sample_accession: DRS019564
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019565
sample_accession: DRS019565
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019566
sample_accession: DRS019566
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019567
sample_accession: DRS019567
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019568
sample_accession: DRS019568
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019569
sample_accession: DRS019569
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019570
sample_accession: DRS019570
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019571
sample_accession: DRS019571
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019572
sample_accession: DRS019572
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019573
sample_accession: DRS019573
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019574
sample_accession: DRS019574
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019575
sample_accession: DRS019575
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019576
sample_accession: DRS019576
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019577
sample_accession: DRS019577
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019578
sample_accession: DRS019578
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019579
sample_accession: DRS019579
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019580
sample_accession: DRS019580
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019581
sample_accession: DRS019581
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019582
sample_accession: DRS019582
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019583
sample_accession: DRS019583
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019584
sample_accession: DRS019584
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019585
sample_accession: DRS019585
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019586
sample_accession: DRS019586
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019587
sample_accession: DRS019587
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019588
sample_accession: DRS019588
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019589
sample_accession: DRS019589
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019590
sample_accession: DRS019590
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019591
sample_accession: DRS019591
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019592
sample_accession: DRS019592
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019593
sample_accession: DRS019593
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019594
sample_accession: DRS019594
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019595
sample_accession: DRS019595
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019596
sample_accession: DRS019596
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019597
sample_accession: DRS019597
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: DRS019598
sample_accession: DRS019598
center_name: OSAKA_PREF
scientific_name: Solanum lycopersicum
submission_accession: DRA003528
sradb_updated: 2016-11-20 05:22:10
sample_attribute:
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


sample_alias: E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationary
sample_accession: ERS016115
broker_name: ArrayExpress
center_name: Genomics Core Facility, EMBL, Heidelberg, Germany
scientific_name: Escherichia coli
sample_attribute: Organism: Escherichia coli || StrainOrLine: K-12 substr. MG1655 || Genotype: wide_type
submission_accession: ERA014184
sradb_updated: 2016-11-20 05:31:37
description:
Protocols: 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 37Â¡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, 4Â¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80Â¡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 50Âµl 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).


sample_alias: E-MTAB-552:Mature Tuber
sample_accession: ERS023593
broker_name: ArrayExpress
center_name: Aalborg University, Denmark
scientific_name: Solanum tuberosum
submission_accession: ERA021569
sradb_updated: 2016-11-20 05:37:06
description:
Protocols: 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.

sample_attribute:
Organism: Solanum tuberosum || OrganismPart: tuber || DevelopmentalStage: mature || BioSourceType: fresh_sample


sample_alias: E-MTAB-552:Young Tuber
sample_accession: ERS023595
broker_name: ArrayExpress
center_name: Aalborg University, Denmark
scientific_name: Solanum tuberosum
submission_accession: ERA021569
sradb_updated: 2016-11-20 05:37:06
description:
Protocols: 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.

sample_attribute:
Organism: Solanum tuberosum || OrganismPart: tuber || DevelopmentalStage: young || BioSourceType: fresh_sample


sample_alias: E-MTAB-861:Central starchy endosperm 4
sample_accession: ERS074999
broker_name: ArrayExpress
center_name: GATC BIOTECH AG
scientific_name: Triticum aestivum
submission_accession: ERA070843
sradb_updated: 2016-11-20 05:51:46
description:
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).

sample_attribute:
Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 21 d || OrganismPart: starchy endosperm


sample_alias: E-MTAB-861:Central starchy endosperm 2
sample_accession: ERS075000
broker_name: ArrayExpress
center_name: GATC BIOTECH AG
scientific_name: Triticum aestivum
submission_accession: ERA070843
sradb_updated: 2016-11-20 05:51:46
description:
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).

sample_attribute:
Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 14 d || OrganismPart: starchy endosperm


sample_alias: E-MTAB-861:Central starchy endosperm 5
sample_accession: ERS075001
broker_name: ArrayExpress
center_name: GATC BIOTECH AG
scientific_name: Triticum aestivum
submission_accession: ERA070843
sradb_updated: 2016-11-20 05:51:46
description:
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).

sample_attribute:
Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 28 d || OrganismPart: starchy endosperm


sample_alias: E-MTAB-861:Central starchy endosperm 1
sample_accession: ERS075002
broker_name: ArrayExpress
center_name: GATC BIOTECH AG
scientific_name: Triticum aestivum
submission_accession: ERA070843
sradb_updated: 2016-11-20 05:51:46
sample_attribute:
Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 10 d || OrganismPart: starchy endosperm


sample_alias: E-MTAB-861:Central starchy endosperm 3
sample_accession: ERS075003
broker_name: ArrayExpress
center_name: GATC BIOTECH AG
scientific_name: Triticum aestivum
submission_accession: ERA070843
sradb_updated: 2016-11-20 05:51:46
sample_attribute:
Organism: Triticum aestivum || InitialTimePoint: anthesis || Age: 17 d || OrganismPart: starchy endosperm


sample_alias: E-MTAB-1585:7sk_3a
sample_accession: ERS225445
broker_name: ArrayExpress
center_name: EMBL-EBI
scientific_name: Mus musculus
sample_attribute: Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal
submission_accession: ERA203799
sradb_updated: 2016-11-20 06:37:18
description:
Protocols: 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.


sample_alias: E-MTAB-1585:7sk_1c
sample_accession: ERS225446
broker_name: ArrayExpress
center_name: EMBL-EBI
scientific_name: Mus musculus
sample_attribute: Organism: Mus musculus || cell type: Embryonic stem cell || strain: 129/Ola || phenotype: normal
submission_accession: ERA203799
sradb_updated: 2016-11-20 06:37:18
description:
Protocols: 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.


sample_alias: 20527
sample_accession: SRS000017
center_name: WUGSC
scientific_name: Streptococcus infantarius subsp. infantarius ATCC BAA-102
xref_link: bioproject: 20527
submission_accession: SRA000246
sradb_updated: 2016-11-20 10:07:54
description:
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.

sample_url_link:
DNA Source: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-102&Template=bacteria

sample_attribute:
finishing 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


sample_alias: PRJNA39289.MEWO
sample_accession: SRS003453
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: MEWO || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.M980928
sample_accession: SRS003454
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: M980928 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.M990514
sample_accession: SRS003455
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: M990514 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.M000216
sample_accession: SRS003456
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: M000216 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.M990802
sample_accession: SRS003457
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: M990802 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.M980409
sample_accession: SRS003458
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: M980409 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.M970109
sample_accession: SRS003459
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: M970109 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.M010403
sample_accession: SRS003460
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: M010403 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.501 MEL
sample_accession: SRS003461
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: 501 MEL || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.M000921
sample_accession: SRS003462
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: M000921 || geographic location (country and/or sea,region): missing || isolation source: Melanoma || strain: missing


sample_alias: PRJNA39289.K-562-4
sample_accession: SRS003463
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: K-562-4 || geographic location (country and/or sea,region): missing || isolation source: K-562 || strain: missing


sample_alias: PRJNA39289.K-562-3
sample_accession: SRS003464
center_name: BI
scientific_name: Homo sapiens
common_name: n/a
anonymized_name: n/a
individual_name: n/a
submission_accession: SRA009053
sradb_updated: 2016-11-20 10:08:56
sample_attribute:
Sample name: K-562-3 || geographic location (country and/or sea,region): missing || isolation source: K-562 || strain: missing


sample_alias: double-haploid rainbow trout
sample_accession: SRS004650
center_name: West Virginia University,
scientific_name: Oncorhynchus mykiss
submission_accession: SRA009276
sradb_updated: 2016-11-20 10:09:03
description:
Tissues 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.


sample_alias: 14710B-2
sample_accession: SRS2456861
scientific_name: Homo sapiens
xref_link: bioproject: 399772: PRJNA399772
submission_accession: SRA602313
sradb_updated: 2017-08-24 20:05:21
sample_attribute:
isolate: control2 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human


sample_alias: 14710B-3
sample_accession: SRS2456862
scientific_name: Homo sapiens
xref_link: bioproject: 399772: PRJNA399772
submission_accession: SRA602313
sradb_updated: 2017-08-24 20:05:21
sample_attribute:
isolate: treat1 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human


sample_alias: 14710B-1
sample_accession: SRS2456863
scientific_name: Homo sapiens
xref_link: bioproject: 399772: PRJNA399772
submission_accession: SRA602313
sradb_updated: 2017-08-24 20:05:21
sample_attribute:
isolate: control1 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human


sample_alias: 14710B-4
sample_accession: SRS2456864
scientific_name: Homo sapiens
xref_link: bioproject: 399772: PRJNA399772
submission_accession: SRA602313
sradb_updated: 2017-08-24 20:05:21
sample_attribute:
isolate: treat2 || age: missing || biomaterial_provider: missing || sex: missing || tissue: missing || cell_line: MCF-7 || BioSampleModel: Human


sample_alias: RNA49
sample_accession: SRS2484887
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 910265.001 || cultivar: Rotuma || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: RNA39
sample_accession: SRS2484888
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 790485.001 || cultivar: Puupuu || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: EW3
sample_accession: SRS2484889
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 30042.001 || cultivar: Toneno || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA38
sample_accession: SRS2484890
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 880690.001 || cultivar: Kea || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: RNA2
sample_accession: SRS2484891
scientific_name: Artocarpus camansi
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 910280.001 || cultivar: Meikole || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA37
sample_accession: SRS2484892
scientific_name: Artocarpus camansi
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 980212.001 || cultivar: Camansi || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA5
sample_accession: SRS2484893
scientific_name: Artocarpus camansi
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 770444.001 || cultivar: Camansi || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA34
sample_accession: SRS2484894
scientific_name: Artocarpus camansi
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 890455.001 || cultivar: Ulu fatu || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA7
sample_accession: SRS2484895
scientific_name: Artocarpus mariannensis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 900252.002 || cultivar: Dugdug || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: EW2
sample_accession: SRS2484896
scientific_name: Artocarpus camansi
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 501.005 || cultivar: Kapiak || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: EW4
sample_accession: SRS2484897
scientific_name: Artocarpus camansi
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 501 || cultivar: Kapiak || dev_stage: Seedling || geo_loc_name: USA: Hawaii || tissue: Root, Stem, and Leaf || BioSampleModel: Plant


sample_alias: RNA35
sample_accession: SRS2484898
scientific_name: Artocarpus camansi
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 389.001 || cultivar: Kapiak || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA48
sample_accession: SRS2484899
scientific_name: Artocarpus altilis x Artocarpus mariannensis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 890184.001 || cultivar: Luthar || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: RNA16
sample_accession: SRS2484900
scientific_name: Artocarpus altilis x Artocarpus mariannensis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 890183.001 || cultivar: Midolab || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: RNA21
sample_accession: SRS2484901
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 900265.001 || cultivar: Karawa || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA24
sample_accession: SRS2484902
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 900261.001 || cultivar: Samoan 2 || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: RNA10
sample_accession: SRS2484903
scientific_name: Artocarpus altilis x Artocarpus mariannensis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 790490.001 || cultivar: Rotuma || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: EW1
sample_accession: SRS2484904
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 970236 || cultivar: Ulu fiti || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA32
sample_accession: SRS2484905
scientific_name: Artocarpus altilis x Artocarpus mariannensis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 890174.001 || cultivar: Ulu afa || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA36
sample_accession: SRS2484906
scientific_name: Artocarpus altilis x Artocarpus mariannensis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 890173.002 || cultivar: Ulu afa elise || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Perianth || BioSampleModel: Plant


sample_alias: RNA40
sample_accession: SRS2484907
scientific_name: Artocarpus altilis x Artocarpus mariannensis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 910269.001 || cultivar: Faine || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: RNA17
sample_accession: SRS2484908
scientific_name: Artocarpus altilis x Artocarpus mariannensis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 790487.001 || cultivar: Unk (Huehue) || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: RNA25
sample_accession: SRS2484909
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 890479.002 || cultivar: Meisei || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: RNA26
sample_accession: SRS2484910
scientific_name: Artocarpus altilis
xref_link: bioproject: 311339: PRJNA311339
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
isolate: 890167.002 || cultivar: Meisaip || dev_stage: Mature || geo_loc_name: USA: Hawaii || tissue: Leaf || BioSampleModel: Plant


sample_alias: A6
sample_accession: SRS2484926
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: A5
sample_accession: SRS2484927
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: A4
sample_accession: SRS2484928
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: A1
sample_accession: SRS2484929
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: D5
sample_accession: SRS2484930
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: A3
sample_accession: SRS2484931
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: A2
sample_accession: SRS2484932
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: D1
sample_accession: SRS2484933
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: D2
sample_accession: SRS2484934
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: D4
sample_accession: SRS2484935
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: D3
sample_accession: SRS2484936
scientific_name: Homo sapiens
xref_link: bioproject: 399503: PRJNA399503
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:59:56
sample_attribute:
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


sample_alias: GSM2791399
sample_accession: SRS2534921
scientific_name: Homo sapiens
xref_link: bioproject: 411985: PRJNA411985
submission_accession: SRA612572
sradb_updated: 2017-10-05 20:45:55
sample_attribute:
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


sample_alias: GSM2791403
sample_accession: SRS2534924
scientific_name: Homo sapiens
xref_link: bioproject: 411985: PRJNA411985
submission_accession: SRA612572
sradb_updated: 2017-10-05 20:45:55
sample_attribute:
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


sample_alias: GSM2791560
sample_accession: SRS2535690
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Total mRNA || barcode: O097 || replicate: Biological replicate 1


sample_alias: GSM2791561
sample_accession: SRS2535691
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Total mRNA || barcode: O098 || replicate: Biological replicate 1


sample_alias: GSM2791562
sample_accession: SRS2535692
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: O099 || replicate: Biological replicate 1


sample_alias: GSM2791563
sample_accession: SRS2535693
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: O100 || replicate: Biological replicate 1


sample_alias: GSM2791564
sample_accession: SRS2535694
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O101 || replicate: Biological replicate 1


sample_alias: GSM2791565
sample_accession: SRS2535695
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: O102 || replicate: Biological replicate 1


sample_alias: GSM2791566
sample_accession: SRS2535696
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: O103 || replicate: Biological replicate 1


sample_alias: GSM2791568
sample_accession: SRS2535697
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Total mRNA || barcode: O105 || replicate: Biological replicate 2


sample_alias: GSM2791567
sample_accession: SRS2535698
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: O104 || replicate: Biological replicate 1


sample_alias: GSM2791570
sample_accession: SRS2535699
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: O107 || replicate: Biological replicate 2


sample_alias: GSM2791569
sample_accession: SRS2535700
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Total mRNA || barcode: O106 || replicate: Biological replicate 2


sample_alias: GSM2791571
sample_accession: SRS2535701
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: O108 || replicate: Biological replicate 2


sample_alias: GSM2791572
sample_accession: SRS2535702
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O109 || replicate: Biological replicate 2


sample_alias: GSM2791573
sample_accession: SRS2535703
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: O110 || replicate: Biological replicate 2


sample_alias: GSM2791574
sample_accession: SRS2535704
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: O111 || replicate: Biological replicate 2


sample_alias: GSM2791575
sample_accession: SRS2535705
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: O112 || replicate: Biological replicate 2


sample_alias: GSM2791576
sample_accession: SRS2535706
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Total mRNA || barcode: U774 || replicate: Biological replicate 1


sample_alias: GSM2791577
sample_accession: SRS2535707
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Total mRNA || barcode: U775 || replicate: Biological replicate 1


sample_alias: GSM2791578
sample_accession: SRS2535708
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: U776 || replicate: Biological replicate 1


sample_alias: GSM2791579
sample_accession: SRS2535709
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: U777 || replicate: Biological replicate 1


sample_alias: GSM2791580
sample_accession: SRS2535710
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Polysomal mRNA || barcode: U778 || replicate: Biological replicate 1


sample_alias: GSM2791581
sample_accession: SRS2535711
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: U779 || replicate: Biological replicate 1


sample_alias: GSM2791582
sample_accession: SRS2535712
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: U780 || replicate: Biological replicate 1


sample_alias: GSM2791583
sample_accession: SRS2535713
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: U781 || replicate: Biological replicate 1


sample_alias: GSM2791584
sample_accession: SRS2535714
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Total mRNA || barcode: U782 || replicate: Biological replicate 2


sample_alias: GSM2791585
sample_accession: SRS2535715
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Total mRNA || barcode: U783 || replicate: Biological replicate 2


sample_alias: GSM2791586
sample_accession: SRS2535716
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Total mRNA || barcode: U784 || replicate: Biological replicate 2


sample_alias: GSM2791587
sample_accession: SRS2535717
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Total mRNA || barcode: U785 || replicate: Biological replicate 2


sample_alias: GSM2791588
sample_accession: SRS2535718
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia || fraction: Polysomal mRNA || barcode: U786 || replicate: Biological replicate 2


sample_alias: GSM2791589
sample_accession: SRS2535719
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia || fraction: Polysomal mRNA || barcode: U787 || replicate: Biological replicate 2


sample_alias: GSM2791590
sample_accession: SRS2535720
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Normoxia+PP242 || fraction: Polysomal mRNA || barcode: U788 || replicate: Biological replicate 2


sample_alias: GSM2791591
sample_accession: SRS2535721
scientific_name: Homo sapiens
xref_link: bioproject: 412005: PRJNA412005
submission_accession: SRA612618
sradb_updated: 2017-10-05 20:45:57
sample_attribute:
source_name: Breast Tissue || cell line: MDA-MB-231 || treatment: Hypoxia+PP242 || fraction: Polysomal mRNA || barcode: U789 || replicate: Biological replicate 2


sample_alias: Pat4037N
sample_accession: SRS2554649
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4037_ID7_Norm || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat4024C
sample_accession: SRS2554650
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4024_ID19_PrimTum || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat4024M
sample_accession: SRS2554651
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4024_ID19_Met || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat4024N
sample_accession: SRS2554652
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4024_ID19_Norm || age: 53y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat4037C
sample_accession: SRS2554653
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4037_ID7_PrimTum || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat235N
sample_accession: SRS2554654
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_235_Norm || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat4005C
sample_accession: SRS2554655
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4005_ID8_PrimTum || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat4005M
sample_accession: SRS2554656
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4005_ID8_Met || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human


sample_alias: Pat4005N
sample_accession: SRS2554657
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4005_ID8_Norm || age: 63y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat224C
sample_accession: SRS2554658
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
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


sample_alias: Pat170N
sample_accession: SRS2554659
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_179_Norm || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat224N
sample_accession: SRS2554660
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_224_Norm || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat224M
sample_accession: SRS2554661
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_224_Met || age: 44y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lymph node || BioSampleModel: Human


sample_alias: Pat067N
sample_accession: SRS2554662
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_067_Norm || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat170M
sample_accession: SRS2554663
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_170_Met || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human


sample_alias: Pat170C
sample_accession: SRS2554664
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_170_PrimTum || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat235M
sample_accession: SRS2554665
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_235_Met || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Skin || BioSampleModel: Human


sample_alias: Pat235C
sample_accession: SRS2554666
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_235_PrimTum || age: 52y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat059N
sample_accession: SRS2554667
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_059_Norm || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat059M
sample_accession: SRS2554668
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_059_Met || age: 46y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lymph node || BioSampleModel: Human


sample_alias: Pat066M
sample_accession: SRS2554669
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_066_Met || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human


sample_alias: Pat066C
sample_accession: SRS2554670
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_066_PrimTum || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat044M
sample_accession: SRS2554671
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_044_Met || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Liver || BioSampleModel: Human


sample_alias: Pat044C
sample_accession: SRS2554672
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_044_PrimTum || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat059C
sample_accession: SRS2554673
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
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


sample_alias: Pat044N
sample_accession: SRS2554674
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_044_Norm || age: 42y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat067C
sample_accession: SRS2554675
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_067_PrimTum || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Breast || BioSampleModel: Human


sample_alias: Pat066N
sample_accession: SRS2554676
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_066_Norm || age: 34y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Blood || BioSampleModel: Human


sample_alias: Pat4037M
sample_accession: SRS2554677
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: Prospective_4037_ID7_Met || age: 43y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Bone || BioSampleModel: Human


sample_alias: Pat067M
sample_accession: SRS2554678
scientific_name: Homo sapiens
submission_accession: SRA615716
sradb_updated: 2017-10-19 20:02:07
sample_attribute:
isolate: TEX_067_Met || age: 48y || biomaterial_provider: Jonas Bergh, Radiumhemmet, Karolinska Institute, SE-171 76 Stockholm || sex: female || tissue: Lung || BioSampleModel: Human


sample_alias: GSM2806527
sample_accession: SRS2571283
scientific_name: Homo sapiens
xref_link: bioproject: 413548: PRJNA413548
submission_accession: SRA617783
sradb_updated: 2017-10-12 20:16:58
sample_attribute:
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


sample_alias: GSM2806528
sample_accession: SRS2571284
scientific_name: Homo sapiens
xref_link: bioproject: 413548: PRJNA413548
submission_accession: SRA617783
sradb_updated: 2017-10-12 20:16:58
sample_attribute:
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


sample_alias: GSM2806530
sample_accession: SRS2571286
scientific_name: Homo sapiens
xref_link: bioproject: 413548: PRJNA413548
submission_accession: SRA617783
sradb_updated: 2017-10-12 20:16:58
sample_attribute:
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


sample_alias: GSM2806559
sample_accession: SRS2572536
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 1 hr || biological replicate: 1


sample_alias: GSM2806560
sample_accession: SRS2572537
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 1 hr || biological replicate: 2


sample_alias: GSM2806561
sample_accession: SRS2572538
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 3 hr || biological replicate: 1


sample_alias: GSM2806562
sample_accession: SRS2572539
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 3 hr || biological replicate: 2


sample_alias: GSM2806563
sample_accession: SRS2572540
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 5 hr || biological replicate: 1


sample_alias: GSM2806564
sample_accession: SRS2572541
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 5 hr || biological replicate: 2


sample_alias: GSM2806565
sample_accession: SRS2572542
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 7 hr || biological replicate: 1


sample_alias: GSM2806566
sample_accession: SRS2572543
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 7 hr || biological replicate: 2


sample_alias: GSM2806567
sample_accession: SRS2572544
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 9 hr || biological replicate: 1


sample_alias: GSM2806568
sample_accession: SRS2572545
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 9 hr || biological replicate: 2


sample_alias: GSM2806569
sample_accession: SRS2572546
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 11 hr || biological replicate: 1


sample_alias: GSM2806570
sample_accession: SRS2572547
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 100 nM dexamethasone || duration of treatment: 11 hr || biological replicate: 2


sample_alias: GSM2806571
sample_accession: SRS2572548
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 1 hr || biological replicate: 1


sample_alias: GSM2806572
sample_accession: SRS2572549
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 1 hr || biological replicate: 2


sample_alias: GSM2806573
sample_accession: SRS2572550
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 3 hr || biological replicate: 1


sample_alias: GSM2806574
sample_accession: SRS2572551
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 3 hr || biological replicate: 2


sample_alias: GSM2806575
sample_accession: SRS2572552
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 5 hr || biological replicate: 1


sample_alias: GSM2806576
sample_accession: SRS2572553
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 5 hr || biological replicate: 2


sample_alias: GSM2806577
sample_accession: SRS2572554
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 7 hr || biological replicate: 1


sample_alias: GSM2806578
sample_accession: SRS2572555
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 7 hr || biological replicate: 2


sample_alias: GSM2806579
sample_accession: SRS2572556
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 9 hr || biological replicate: 1


sample_alias: GSM2806580
sample_accession: SRS2572557
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 9 hr || biological replicate: 2


sample_alias: GSM2806581
sample_accession: SRS2572558
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 11 hr || biological replicate: 1


sample_alias: GSM2806582
sample_accession: SRS2572559
scientific_name: Homo sapiens
xref_link: bioproject: 413586: PRJNA413586
submission_accession: SRA617809
sradb_updated: 2017-10-12 20:17:01
sample_attribute:
source_name: A549 cell line || cell line: A549 || treatment: 0.02% v/v ethanol || duration of treatment: 11 hr || biological replicate: 2


sample_alias: GSM2806688
sample_accession: SRS2574055
scientific_name: Mus musculus
xref_link: bioproject: 413658: PRJNA413658
submission_accession: SRA617887
sradb_updated: 2017-10-12 20:17:03
sample_attribute:
source_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


sample_alias: GSM2806687
sample_accession: SRS2574056
scientific_name: Mus musculus
xref_link: bioproject: 413658: PRJNA413658
submission_accession: SRA617887
sradb_updated: 2017-10-12 20:17:03
sample_attribute:
source_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 (naÃ¯ve)


sample_alias: GSM2806691
sample_accession: SRS2574059
scientific_name: Mus musculus
xref_link: bioproject: 413658: PRJNA413658
submission_accession: SRA617887
sradb_updated: 2017-10-12 20:17:03
sample_attribute:
source_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


sample_alias: GSM2806692
sample_accession: SRS2574060
scientific_name: Mus musculus
xref_link: bioproject: 413658: PRJNA413658
submission_accession: SRA617887
sradb_updated: 2017-10-12 20:17:03
sample_attribute:
source_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


sample_alias: GSM2806694
sample_accession: SRS2574062
scientific_name: Mus musculus
xref_link: bioproject: 413658: PRJNA413658
submission_accession: SRA617887
sradb_updated: 2017-10-12 20:17:03
sample_attribute:
source_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


sample_alias: GSM2806924
sample_accession: SRS2575351
scientific_name: Streptomyces clavuligerus ATCC 27064
xref_link: bioproject: 413703: PRJNA413703
submission_accession: SRA617916
sradb_updated: 2017-10-12 20:17:05
sample_attribute:
source_name: mycelium || phenotype: wildtype || strain: ATCC 27064 || type-material: type strain of Streptomyces clavuligerus


# experiment

experiment_alias: DRX005522
experiment_accession: DRX005522
center_name: NIVTS
title: Transcriptional sequence of 'Ki' from 454
study_name: DRP002494
study_accession: DRP002494
sample_name: DRS005661
sample_accession: DRS005661
library_name: LIY01
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: RANDOM
library_layout: PAIRED - NOMINAL_LENGTH: 450;
platform: LS454
instrument_model: 454 GS FLX Titanium
platform_parameters: INSTRUMENT_MODEL: 454 GS FLX Titanium
submission_accession: DRA000945
sradb_updated: 2016-11-19 08:02:28
read_spec:
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: 1


experiment_alias: DRX005523
experiment_accession: DRX005523
center_name: NIVTS
title: Transcriptional sequence of 'Aka' leaf
study_name: DRP002494
study_accession: DRP002494
sample_name: DRS005662
sample_accession: DRS005662
library_name: Aka_leaf
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: RANDOM
library_layout: PAIRED - NOMINAL_LENGTH: 180;
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
submission_accession: DRA000945
sradb_updated: 2016-11-19 08:02:28
read_spec:
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: 91


experiment_alias: DRX022400
experiment_accession: DRX022400
center_name: KYOTO_SC
title: Illumina MiSeq paired end sequencing of AB
study_name: DRP002820
study_accession: DRP002820
sample_name: DRS021958
sample_accession: DRS021958
library_name: MiSeq_Anterior-blastema
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 338;
platform: ILLUMINA
instrument_model: Illumina MiSeq
platform_parameters: INSTRUMENT_MODEL: Illumina MiSeq
submission_accession: DRA002722
sradb_updated: 2016-11-19 08:06:05
read_spec:
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: 126


experiment_alias: DRX026507
experiment_accession: DRX026507
center_name: MIYAZAKI
title: Illumina HiSeq 2000 paired end sequencing of SAMD00025070
study_name: DRP002612
study_accession: DRP002612
sample_name: DRS019417
sample_accession: DRS019417
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: RANDOM
library_layout: PAIRED - NOMINAL_LENGTH: 300;
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
submission_accession: DRA002992
sradb_updated: 2016-11-19 08:06:38
read_spec:
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: 102


experiment_alias: E-MTAB-387:Transition_to_Stationary
experiment_accession: ERX007969
broker_name: ArrayExpress
center_name: EMBL_Heidelberg
title: RNA sequencing in E. coli K12
study_name: E-MTAB-387
study_accession: ERP000350
design_description: RNA sequencing in E. coli K12
sample_name: E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationary
sample_accession: ERS016115
library_name: Transition_to_Stationary
library_strategy: OTHER
library_source: OTHER
library_selection: cDNA
library_layout: SINGLE -
read_spec: READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: ERA014184
sradb_updated: 2016-11-19 08:11:12
library_construction_protocol:
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 37Â¡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, 4Â¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80Â¡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 50Âµl 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).

experiment_attribute:
Experimental Factor: GENOTYPE: wide_type || Experimental Factor: GROWTHCONDITION: transition-to-stationary-phase


experiment_alias: E-MTAB-552:RHs08
experiment_accession: ERX010637
broker_name: ArrayExpress
title: Illumina Genome Analyzer sequencing; Transcriptome Analysis of the potato (genotype RH89-039-16)
study_name: E-MTAB-552
study_accession: ERP000527
design_description: Transcriptome Analysis of the potato (genotype RH89-039-16)
sample_name: E-MTAB-552:Mature Tuber
sample_accession: ERS023593
library_name: S8
library_strategy: WGS
library_source: TRANSCRIPTOMIC
library_selection: RANDOM
library_layout: SINGLE -
read_spec: READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer
experiment_attribute: Experimental Factor: ORGANISMPART: tuber || Experimental Factor: DEVELOPMENTALSTAGE: mature
submission_accession: ERA021569
sradb_updated: 2016-11-19 08:11:57
library_construction_protocol:
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.


experiment_alias: E-MTAB-861:assay 4
experiment_accession: ERX033523
broker_name: ArrayExpress
center_name: GATC Biotech AG
title: wheat starchy endosperm RNA-Seq
study_name: E-MTAB-861
study_accession: ERP001030
design_description: wheat starchy endosperm RNA-Seq
sample_name: E-MTAB-861:Central starchy endosperm 4
sample_accession: ERS074999
library_name: RNA Extract 4
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
read_spec: READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
experiment_attribute: Experimental Factor: Age: 21 d
submission_accession: ERA070843
sradb_updated: 2016-11-19 08:14:30
library_construction_protocol:
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).


experiment_alias: E-MTAB-1585:7sk_3a
experiment_accession: ERX221944
broker_name: ArrayExpress
center_name: EMBL-EBI
title: Transcriptional profiling of 7SK knockdown in mouse embryonic stem cells
study_name: E-MTAB-1585
study_accession: ERP002405
design_description: Transcriptional profiling of 7SK knockdown in mouse embryonic stem cells
sample_name: E-MTAB-1585:7sk_3a
sample_accession: ERS225445
library_name: 7sk_3a
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: RANDOM
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
experiment_attribute: Experimental Factor: genetic modification: Knockdown (3' ASO)
submission_accession: ERA203799
sradb_updated: 2016-11-19 08:27:00
library_construction_protocol:
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.


experiment_alias: E-MTAB-1585:7sk_1c
experiment_accession: ERX221945
broker_name: ArrayExpress
center_name: EMBL-EBI
title: Transcriptional profiling of 7SK knockdown in mouse embryonic stem cells
study_name: E-MTAB-1585
study_accession: ERP002405
design_description: Transcriptional profiling of 7SK knockdown in mouse embryonic stem cells
sample_name: E-MTAB-1585:7sk_1c
sample_accession: ERS225446
library_name: 7sk_1c
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: RANDOM
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
experiment_attribute: Experimental Factor: genetic modification: none
submission_accession: ERA203799
sradb_updated: 2016-11-19 08:27:00
library_construction_protocol:
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.


experiment_alias: exp_1.GAC.AIG_AOTS_GWDJGJ101
experiment_accession: ERX234949
center_name: GSC
title: Adineta vaga Titanium Simple
study_name: study_AIG
study_accession: ERP002474
sample_name: sample_AIG_104782
sample_accession: ERS235800
library_name: AIGAOTS
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
library_construction_protocol: none provided
platform: LS454
instrument_model: 454 GS FLX Titanium
platform_parameters: INSTRUMENT_MODEL: 454 GS FLX Titanium
submission_accession: ERA206999
sradb_updated: 2016-11-19 08:28:11
read_spec:
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: 5


experiment_alias: 2036533341
experiment_accession: SRX000121
center_name: WUGSC
title: 454 sequencing of Tachyglossus aculeatus transcript fragment library
study_name: 2036532902, 2036545831
study_accession: SRP000098
design_description: none provided
sample_name: Tachyglossus aculeatus
sample_accession: SRS000290
library_name: 2036533341
library_strategy: FL-cDNA
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: LS454
instrument_model: 454 GS FLX
platform_parameters: INSTRUMENT_MODEL: 454 GS FLX
experiment_attribute: submission_id: SRA000241
submission_accession: SRA000241
sradb_updated: 2016-11-19 10:37:45
read_spec:
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: 5


experiment_alias: 2140631529
experiment_accession: SRX000023
center_name: WUGSC
study_name: 2140628333
study_accession: SRP000017
design_description: none provided
sample_name: Streptococcus infantarius subsp. infantarius ATCC BAA-102
sample_accession: SRS000017
library_name: 2140631529
library_strategy: WGS
library_source: GENOMIC
library_selection: RANDOM
library_layout: SINGLE -
platform: LS454
instrument_model: 454 GS FLX
platform_parameters: INSTRUMENT_MODEL: 454 GS FLX
experiment_attribute: submission_id: SRA000246
submission_accession: SRA000246
sradb_updated: 2016-11-19 10:37:45
title:
454 sequencing of Streptococcus infantarius subsp. infantarius ATCC BAA-102 genomic fragment library

read_spec:
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: 5


experiment_alias: 30BV1AAXX080828-1-P
experiment_accession: SRX006122
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003453
library_name: Solexa-7012
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'

read_spec:
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: 52

experiment_attribute:
analysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17302


experiment_alias: 30BV1AAXX080828-2-P
experiment_accession: SRX006123
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003454
library_name: Solexa-7011
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7011' containing sample 'M980928'

read_spec:
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: 52

experiment_attribute:
analysis_type: cDNA || gssr_id: 26771.0 || lsid: BROAD:SEQUENCING_SAMPLE:26771.0 || material_type: New Tech Library || project: G1681 || work_request: 17302


experiment_alias: 30BV1AAXX080828-3-P
experiment_accession: SRX006124
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003455
library_name: Solexa-7010
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7010' containing sample 'M990514'

read_spec:
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: 52

experiment_attribute:
analysis_type: cDNA || gssr_id: 26770.0 || lsid: BROAD:SEQUENCING_SAMPLE:26770.0 || material_type: New Tech Library || project: G1681 || work_request: 17302


experiment_alias: 30BV1AAXX080828-5-P
experiment_accession: SRX006125
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003456
library_name: Solexa-7009
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7009' containing sample 'M000216'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26769.0 || lsid: BROAD:SEQUENCING_SAMPLE:26769.0 || material_type: New Tech Library || project: G1681 || work_request: 17302


experiment_alias: 30BV1AAXX080828-6-P
experiment_accession: SRX006126
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003457
library_name: Solexa-7008
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7008' containing sample 'M990802'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26768.0 || lsid: BROAD:SEQUENCING_SAMPLE:26768.0 || material_type: New Tech Library || project: G1681 || work_request: 17302


experiment_alias: 30BV1AAXX080828-7-P
experiment_accession: SRX006127
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003458
library_name: Solexa-7007
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7007' containing sample 'M980409'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26767.0 || lsid: BROAD:SEQUENCING_SAMPLE:26767.0 || material_type: New Tech Library || project: G1681 || work_request: 17302


experiment_alias: 30BV1AAXX080828-8-P
experiment_accession: SRX006128
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003459
library_name: Solexa-7006
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7006' containing sample 'M970109'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26766.0 || lsid: BROAD:SEQUENCING_SAMPLE:26766.0 || material_type: New Tech Library || project: G1681 || work_request: 17302


experiment_alias: 30C3WAAXX080918-1-P
experiment_accession: SRX006129
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003453
library_name: Solexa-7012
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7012' containing sample 'MEWO'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26772.0 || lsid: BROAD:SEQUENCING_SAMPLE:26772.0 || material_type: New Tech Library || project: G1681 || work_request: 17462


experiment_alias: 30C3WAAXX080918-3-P
experiment_accession: SRX006131
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003460
library_name: Solexa-7005
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7005' containing sample 'M010403'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26765.0 || lsid: BROAD:SEQUENCING_SAMPLE:26765.0 || material_type: New Tech Library || project: G1681 || work_request: 17461


experiment_alias: 30C3WAAXX080918-5-P
experiment_accession: SRX006132
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003461
library_name: Solexa-7013
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7013' containing sample '501 MEL'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26773.0 || lsid: BROAD:SEQUENCING_SAMPLE:26773.0 || material_type: New Tech Library || project: G1681 || work_request: 17461


experiment_alias: 30C3WAAXX080918-6-P
experiment_accession: SRX006133
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003462
library_name: Solexa-7014
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7014' containing sample 'M000921'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26774.0 || lsid: BROAD:SEQUENCING_SAMPLE:26774.0 || material_type: New Tech Library || project: G1681 || work_request: 17461


experiment_alias: 30C3WAAXX080918-7-P
experiment_accession: SRX006134
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003463
library_name: Solexa-7015
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 500;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7015' containing sample 'K-562-4'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26775.0 || lsid: BROAD:SEQUENCING_SAMPLE:26775.0 || material_type: New Tech Library || project: G1681 || work_request: 17461


experiment_alias: 30C3WAAXX080918-8-P
experiment_accession: SRX006135
center_name: BI
study_accession: SRP000931
design_description: Illumina sequencing of Homo sapiens via complementary DNA
sample_accession: SRS003464
library_name: Solexa-7016
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED - NOMINAL_LENGTH: 350;
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
submission_accession: SRA009053
sradb_updated: 2016-11-19 10:39:16
title:
Illumina whole genome shotgun sequencing of null paired-end library 'Solexa-7016' containing sample 'K-562-3'

experiment_attribute:
analysis_type: cDNA || gssr_id: 26776.0 || lsid: BROAD:SEQUENCING_SAMPLE:26776.0 || material_type: New Tech Library || project: G1681 || work_request: 17461


experiment_alias: Rainbow trout transcriptome analysis using Sanger and 454-Pyrosequencing approaches
experiment_accession: SRX007396
center_name: West Virginia University,
title: Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approaches
study_accession: SRP001007
sample_accession: SRS004650
library_name: 454
library_strategy: EST
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: LS454
instrument_model: 454 GS FLX
platform_parameters: INSTRUMENT_MODEL: 454 GS FLX
submission_accession: SRA009276
sradb_updated: 2016-11-19 10:39:43
design_description:
Messenger 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 SuperScriptÂ® Double-Stranded cDNA Synthesis Kit (Invitrogen, CA) with 100 ÂµM 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 Âµl water, 10 Âµl 10x T4 DNA Ligase buffer (NEB), 4 Âµl 10 mM dNTP mix, 5 Âµl T4 DNA polymerase (3 U/Âµl) (NEB), 1 Âµl Klenow polymerase (5 U/ Âµl) (NEB), and 5 Âµl Polynucleotide kinase (10 U/Âµl) (NEB) and cleaned up with a Qiaquick PCR minelute column and eluted in 32ul EB. A dA-overhang was added at 3â€™ end of cDNA by adding the following to the blunt-ended cDNA: 5 Âµl 10x buffer 2 (NEB), 10 Âµl 1 mM dATP and 3 Âµl Klenow exo-minus polymerase (5 U/Âµl) (NEB). The reaction was incubated at 370C for 30 minutes and then cleaned up with a QIAquick MiniElute column and eluted in 10 Âµl EB. The cDNA was adaptored with Titanium adaptors (Roche/454 Life Sciences, CT) by adding 9 Âµl water, 25 Âµl 2x Rapid Ligase buffer (Enzymatics, MA) 5 Âµl (50 ÂµM) Titanium adapter A/B mix and 1 Âµl T4 DNA Ligase (600 U/Âµl (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 Âµl 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 Qiagenâ€™s Gel Extraction kit and the cDNA was eluted in 30 Âµl EB. One Âµl of the gel- purified cDNA was used as template for amplification in 50 Âµl PCR reactions containing 10 Âµl 5x Phusion Buffer HF (NEB), 25 ÂµM Adapter A_For primer (5â€™CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGT3â€™), 25 ÂµM Adapter B_For primer (5â€™CCTATCCCCTGTGTGCCTTGGCAGTCTCAGT3â€™), 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 Â¼ units of duplex specific nuclease (DSN). The normalized cDNA was then amplified from 1 Âµl 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.


experiment_alias: RNA49
experiment_accession: SRX3153033
title: RNA-Seq of Artocarpus altilis leaf
study_accession: SRP116664
sample_accession: SRS2484887
library_name: RNA49
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
submission_accession: SRA604752
sradb_updated: 2017-09-07 19:18:55
design_description:
Ribo-Zero rRNA Removal Kit, ScriptSeq v2 RNA-Seq Library Preparation Kit, AMPureXP beads, Illumina HiSeq 2000 paired-end sequencing


experiment_alias: A6
experiment_accession: SRX3153076
title: aneuploid tumor 6
study_accession: SRP116668
sample_accession: SRS2484926
library_name: A6
library_strategy: WXS
library_source: GENOMIC
library_selection: Hybrid Selection
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: NextSeq 500
platform_parameters: INSTRUMENT_MODEL: NextSeq 500
submission_accession: SRA604756
sradb_updated: 2017-09-07 19:18:55
design_description:
DNA 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.


experiment_alias: GSM2791399
experiment_accession: SRX3209939
title: GSM2791399: HBCx-22 PDX treated with vehicle #1; Homo sapiens; RNA-Seq
study_name: GSE104177
study_accession: SRP118776
sample_accession: SRS2534921
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2500
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2500
xref_link: gds: 302791399: GSM2791399
submission_accession: SRA612572
sradb_updated: 2017-10-12 19:16:19
library_construction_protocol:
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 2Ã—50bp paired end sequencing on an Illumina sequencing platform.


experiment_alias: GSM2791560
experiment_accession: SRX3210843
title: GSM2791560: 37NormTotal; Homo sapiens; RNA-Seq
study_name: GSE104193
study_accession: SRP118788
sample_accession: SRS2535690
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
xref_link: gds: 302791560: GSM2791560
experiment_attribute: GEO Accession: GSM2791560
submission_accession: SRA612618
sradb_updated: 2017-10-12 19:16:22
library_construction_protocol:
Polysomal mRNA was obtained by 10%â€“50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1Ã— 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 Î¼g/ml cycloheximide, 2.5 Î¼l/mL RNAaseOut and 1Ã— Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 Ã— g for 15 minutes at 4Â°C. One microgram of total protein from the supernatant was loaded onto a 10%â€“50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4Â°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 Î¼l 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.,).


experiment_alias: Pat4037M
experiment_accession: SRX3230136
title: Whole Exome Sequencing of breast cancer tumor and metastase
study_accession: SRP119112
sample_accession: SRS2554677
library_name: Pat4037M
library_strategy: OTHER
library_source: GENOMIC
library_selection: Hybrid Selection
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
submission_accession: SRA615716
sradb_updated: 2017-10-19 19:08:31
design_description:
Sure Select Human All Exon V4 (Agilent Technologies) on WGA DNA with GenomiPhi V2 DNA Amplification Kit (GE Healthcare)


experiment_alias: GSM2806527
experiment_accession: SRX3257822
title: GSM2806527: IgG CLIP-seq in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-Seq
study_name: GSE104711
study_accession: SRP119540
sample_accession: SRS2571283
library_strategy: RIP-Seq
library_source: TRANSCRIPTOMIC
library_selection: other
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2500
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2500
xref_link: gds: 302806527: GSM2806527
experiment_attribute: GEO Accession: GSM2806527
submission_accession: SRA617783
sradb_updated: 2017-10-12 19:21:55
library_construction_protocol:
Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4Â°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50Î¼l washed protein A Dynabeads was added per 500Î¼l lysates. Samples were rotated for 2 h at 4Â°C. Discarded the supernatant and washed the beads twice with 900 Î¼l high-salt buffer. Then washed twice with 900 Î¼l wash buffer with different mount of Rnase A (high-RNase concentration: 2Î¼g/ml, moderate-RNase concentration: 1Î¼g/ml and low-RNase concentration: 0.2Î¼g/ml). Beads were washed with 900 Î¼l RNase-free wash buffer twice. Then RNA 3â€™ ends were dephosphorylated. Linkers were ligated to 3â€™ ends of RNAs, 32P-Î³-ATP labeled linker was ligated to the 5 â€™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.


experiment_alias: GSM2806559
experiment_accession: SRX3259103
title: GSM2806559: DEX_1hr_Rep1; Homo sapiens; RNA-Seq
study_name: GSE104714
study_accession: SRP119557
sample_accession: SRS2572536
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
xref_link: gds: 302806559: GSM2806559
experiment_attribute: GEO Accession: GSM2806559
submission_accession: SRA617809
sradb_updated: 2017-10-12 19:21:59
library_construction_protocol:
RNA was extracted with RNeasy Miniprep kit. Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.


experiment_alias: GSM2806589
experiment_accession: SRX3260008
title: GSM2806589: DDL3431_1; Burkholderia pseudomallei; RNA-Seq
study_name: GSE104716
study_accession: SRP119575
sample_accession: SRS2573343
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
xref_link: gds: 302806589: GSM2806589
experiment_attribute: GEO Accession: GSM2806589
submission_accession: SRA617842
sradb_updated: 2017-10-12 19:22:00
library_construction_protocol:
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)


experiment_alias: GSM2806686
experiment_accession: SRX3260744
title: GSM2806686: Naive CD4_1; Mus musculus; RNA-Seq
study_name: GSE104725
study_accession: SRP119595
sample_accession: SRS2574058
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 1500
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 1500
xref_link: gds: 302806686: GSM2806686
experiment_attribute: GEO Accession: GSM2806686
submission_accession: SRA617887
sradb_updated: 2017-10-12 19:22:02
library_construction_protocol:
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 protocols


experiment_alias: GSM2806876
experiment_accession: SRX3262378
title: GSM2806876: Liver - Corn Oil KS1; Mus musculus; RNA-Seq
study_name: GSE104734
study_accession: SRP119609
sample_accession: SRS2575306
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
xref_link: gds: 302806876: GSM2806876
experiment_attribute: GEO Accession: GSM2806876
submission_accession: SRA617912
sradb_updated: 2017-10-12 19:22:04
library_construction_protocol:
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.


experiment_alias: GSM2806924
experiment_accession: SRX3262427
title: GSM2806924: ATCC27064; Streptomyces clavuligerus; RNA-Seq
study_name: GSE104738
study_accession: SRP119613
sample_accession: SRS2575351
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
xref_link: gds: 302806924: GSM2806924
experiment_attribute: GEO Accession: GSM2806924
submission_accession: SRA617916
sradb_updated: 2017-10-12 19:22:04
library_construction_protocol:
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 â€˜Turbo DNA-freeâ€™ 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 manufacturerâ€™s instructions (Illumina).


# run

run_alias: EUGXWLM01
run_accession: SRR000647
run_date: 2007-08-23 00:00:00
run_center: WUGSC
experiment_accession: SRX000121
experiment_name: 2036533341
submission_accession: SRA000241
sradb_updated: 2016-11-19 19:54:28
run_attribute:


run_alias: EXRHO8E05
run_accession: SRR000137
run_date: 2007-10-23 00:00:00
run_center: WUGSC
experiment_accession: SRX000023
experiment_name: 2140631529
submission_accession: SRA000246
sradb_updated: 2016-11-19 19:54:29
run_attribute:


run_alias: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.1
run_accession: SRR018256
run_center: BI
experiment_accession: SRX006122
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.2
run_accession: SRR018257
run_center: BI
experiment_accession: SRX006123
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.3
run_accession: SRR018258
run_center: BI
experiment_accession: SRX006124
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.5
run_accession: SRR018259
run_center: BI
experiment_accession: SRX006125
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.6
run_accession: SRR018260
run_center: BI
experiment_accession: SRX006126
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.7
run_accession: SRR018261
run_center: BI
experiment_accession: SRX006127
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.8
run_accession: SRR018262
run_center: BI
experiment_accession: SRX006128
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.1
run_accession: SRR018263
run_center: BI
experiment_accession: SRX006129
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.2
run_accession: SRR018264
run_center: BI
experiment_accession: SRX006130
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.3
run_accession: SRR018265
run_center: BI
experiment_accession: SRX006131
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.5
run_accession: SRR018266
run_center: BI
experiment_accession: SRX006132
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.6
run_accession: SRR018267
run_center: BI
experiment_accession: SRX006133
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.7
run_accession: SRR018268
run_center: BI
experiment_accession: SRX006134
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


run_alias: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.8
run_accession: SRR018269
run_center: BI
experiment_accession: SRX006135
submission_accession: SRA009053
sradb_updated: 2016-11-19 20:03:15
run_attribute:
analysis_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


# sra

run_alias: E-MTAB-387:Early_Exponential.txt
run_accession: ERR019652
updated_date: 2016-06-28
run_center: Genomics Core Facility, EMBL, Heidelberg, Germany
experiment_name: E-MTAB-387:Early_Exponential
experiment_alias: E-MTAB-387:Early_Exponential
experiment_accession: ERX007970
experiment_title: RNA sequencing in E. coli K12
study_name: E-MTAB-387
sample_name: E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Early_exponential
design_description: RNA sequencing in E. coli K12
library_name: Early_Exponential
library_strategy: OTHER
library_source: OTHER
library_selection: cDNA
library_layout: SINGLE -
read_spec: READ_INDEX: 0; READ_CLASS: Application Read; READ_TYPE: Forward; BASE_COORD: 1
platform: ILLUMINA
instrument_model: Illumina Genome Analyzer II
platform_parameters: INSTRUMENT_MODEL: Illumina Genome Analyzer II
experiment_attribute: Experimental Factor: GENOTYPE: wide_type || Experimental Factor: GROWTHCONDITION: early-exponential
sample_alias: E-MTAB-387:E_coli_K12_MG1655_RNAseq_LB_Early_exponential
sample_accession: ERS016116
sample_attribute: Organism: Escherichia coli || StrainOrLine: K-12 substr. MG1655 || Genotype: wide_type
study_alias: E-MTAB-387
study_accession: ERP000350
study_title: RNA sequencing in E. coli K12
study_type: Other
center_project_name: RNA sequencing in E. coli K12
study_url_link: E-MTAB-387 in ArrayExpress: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MTAB-387
submission_accession: ERA014184
submission_center: EMBL_Heidelberg
library_construction_protocol:
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 37Ã‚Â¡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, 4Ã‚Â¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80Ã‚Â¡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 50Ã‚Âµl 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).

description:
Protocols: 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 37Ã‚Â¡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, 4Ã‚Â¡C), washed in 1xPBS and pellets were snap-frozen and stored at _80Ã‚Â¡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 50Ã‚Âµl 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).

study_description:
Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phase


run_alias: Rainbow trout transcriptome-454-2
run_accession: SRR020740
updated_date: 2013-07-26
experiment_alias: Rainbow trout transcriptome analysis using Sanger and 454-Pyrosequencing approaches
experiment_accession: SRX007396
experiment_title: Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approaches
library_name: 454
library_strategy: EST
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: LS454
instrument_model: 454 GS FLX
platform_parameters: INSTRUMENT_MODEL: 454 GS FLX
sample_alias: double-haploid rainbow trout
sample_accession: SRS004650
study_alias: Trout transcriptome-454
study_accession: SRP001007
study_title: Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approaches
study_type: Other
center_project_name: Oncorhynchus mykiss
submission_accession: SRA009276
submission_center: West Virginia University,
submission_lab: Animal Biotechnology and Genomics
submission_date: 2009-08-05
sradb_updated: 2018-05-10 18:11:11
design_description:
Messenger 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 SuperScriptÃ‚Â® Double-Stranded cDNA Synthesis Kit (Invitrogen, CA) with 100 Ã‚ÂµM 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 Ã‚Âµl water, 10 Ã‚Âµl 10x T4 DNA Ligase buffer (NEB), 4 Ã‚Âµl 10 mM dNTP mix, 5 Ã‚Âµl T4 DNA polymerase (3 U/Ã‚Âµl) (NEB), 1 Ã‚Âµl Klenow polymerase (5 U/ Ã‚Âµl) (NEB), and 5 Ã‚Âµl Polynucleotide kinase (10 U/Ã‚Âµl) (NEB) and cleaned up with a Qiaquick PCR minelute column and eluted in 32ul EB. A dA-overhang was added at 3Ã¢â‚¬â„¢ end of cDNA by adding the following to the blunt-ended cDNA: 5 Ã‚Âµl 10x buffer 2 (NEB), 10 Ã‚Âµl 1 mM dATP and 3 Ã‚Âµl Klenow exo-minus polymerase (5 U/Ã‚Âµl) (NEB). The reaction was incubated at 370C for 30 minutes and then cleaned up with a QIAquick MiniElute column and eluted in 10 Ã‚Âµl EB. The cDNA was adaptored with Titanium adaptors (Roche/454 Life Sciences, CT) by adding 9 Ã‚Âµl water, 25 Ã‚Âµl 2x Rapid Ligase buffer (Enzymatics, MA) 5 Ã‚Âµl (50 Ã‚ÂµM) Titanium adapter A/B mix and 1 Ã‚Âµl T4 DNA Ligase (600 U/Ã‚Âµl (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 Ã‚Âµl 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 QiagenÃ¢â‚¬â„¢s Gel Extraction kit and the cDNA was eluted in 30 Ã‚Âµl EB. One Ã‚Âµl of the gel- purified cDNA was used as template for amplification in 50 Ã‚Âµl PCR reactions containing 10 Ã‚Âµl 5x Phusion Buffer HF (NEB), 25 Ã‚ÂµM Adapter A_For primer (5Ã¢â‚¬â„¢CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGT3Ã¢â‚¬â„¢), 25 Ã‚ÂµM Adapter B_For primer (5Ã¢â‚¬â„¢CCTATCCCCTGTGTGCCTTGGCAGTCTCAGT3Ã¢â‚¬â„¢), 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 Ã‚Â¼ units of duplex specific nuclease (DSN). The normalized cDNA was then amplified from 1 Ã‚Âµl 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.

description:
Tissues 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 TRIzolÃ¢â€žÂ¢ (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.

study_abstract:
Background: 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.


run_alias: GSM2791401_r1
run_accession: SRR6067739
updated_date: 2017-10-11
experiment_name: GSM2791401
experiment_alias: GSM2791401
experiment_accession: SRX3209941
experiment_title: GSM2791401: HBCx-22 PDX treated with vehicle #3; Homo sapiens; RNA-Seq
study_name: GSE104177
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2500
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2500
sample_alias: GSM2791401
sample_accession: SRS2534923
study_alias: GSE104177
study_accession: SRP118776
study_title: Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenografts
study_type: Transcriptome Analysis
center_project_name: GSE104177
submission_accession: SRA612572
submission_comment: submission brokered by GEO
submission_center: GEO
sradb_updated: 2018-05-10 18:11:11
library_construction_protocol:
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 2Ãƒâ€”50bp paired end sequencing on an Illumina sequencing platform.

study_abstract:
These 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 study


run_alias: GSM2791564_r1
run_accession: SRR6068878
updated_date: 2017-10-11
experiment_name: GSM2791564
experiment_alias: GSM2791564
experiment_accession: SRX3210847
experiment_title: GSM2791564: 37NormPoly; Homo sapiens; RNA-Seq
study_name: GSE104193
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: PAIRED -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
experiment_attribute: GEO Accession: GSM2791564
sample_alias: GSM2791564
sample_accession: SRS2535694
study_alias: GSE104193
study_accession: SRP118788
study_type: Transcriptome Analysis
center_project_name: GSE104193
submission_accession: SRA612618
submission_comment: submission brokered by GEO
submission_center: GEO
sradb_updated: 2018-05-10 18:11:11
library_construction_protocol:
Polysomal mRNA was obtained by 10%Ã¢â‚¬â€œ50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1Ãƒâ€” 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 ÃŽÂ¼g/ml cycloheximide, 2.5 ÃŽÂ¼l/mL RNAaseOut and 1Ãƒâ€” Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 Ãƒâ€” g for 15 minutes at 4Ã‚Â°C. One microgram of total protein from the supernatant was loaded onto a 10%Ã¢â‚¬â€œ50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4Ã‚Â°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 ÃŽÂ¼l 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 TruSeqÃ¢â€žÂ¢ RNA Sample Prep Kit v2 (Illumina Inc.,).

sample_attribute:
source_name: Breast Tissue || cell line: MCF10A || treatment: Normoxia || fraction: Polysomal mRNA || barcode: O101 || replicate: Biological replicate 1

study_title:
Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-ÃƒÅ¸ signalling and malignant features in vitro and in vivoÃ‚Â 

study_abstract:
We 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 < Ã¢â‚¬â€œ1.5 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 lines


run_alias: GSM2806527_r1
run_accession: SRR6145773
updated_date: 2017-10-11
experiment_name: GSM2806527
experiment_alias: GSM2806527
experiment_accession: SRX3257822
experiment_title: GSM2806527: IgG CLIP-seq in BCBL-1 cells; Homo sapiens; Human gammaherpesvirus 8; RIP-Seq
study_name: GSE104711
library_strategy: RIP-Seq
library_source: TRANSCRIPTOMIC
library_selection: other
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2500
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2500
experiment_attribute: GEO Accession: GSM2806527
sample_alias: GSM2806527
sample_accession: SRS2571283
study_alias: GSE104711
study_accession: SRP119540
study_title: K8 CLIP-Seq in KSHV reactivated BCBL-1 cells
study_type: Other
center_project_name: GSE104711
submission_accession: SRA617783
submission_comment: submission brokered by GEO
submission_center: GEO
sradb_updated: 2018-05-10 18:11:11
library_construction_protocol:
Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4Ã‚Â°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50ÃŽÂ¼l washed protein A Dynabeads was added per 500ÃŽÂ¼l lysates. Samples were rotated for 2 h at 4Ã‚Â°C. Discarded the supernatant and washed the beads twice with 900 ÃŽÂ¼l high-salt buffer. Then washed twice with 900 ÃŽÂ¼l wash buffer with different mount of Rnase A (high-RNase concentration: 2ÃŽÂ¼g/ml, moderate-RNase concentration: 1ÃŽÂ¼g/ml and low-RNase concentration: 0.2ÃŽÂ¼g/ml). Beads were washed with 900 ÃŽÂ¼l RNase-free wash buffer twice. Then RNA 3Ã¢â‚¬â„¢ ends were dephosphorylated. Linkers were ligated to 3Ã¢â‚¬â„¢ ends of RNAs, 32P-ÃŽÂ³-ATP labeled linker was ligated to the 5 Ã¢â‚¬â„¢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 TruSeqÃ¢â€žÂ¢ RNA and DNA Sample Prep Kits.

sample_attribute:
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

study_abstract:
KSHV 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.


run_alias: GSM2806692_r1
run_accession: SRR6148730
updated_date: 2017-10-11
experiment_name: GSM2806692
experiment_alias: GSM2806692
experiment_accession: SRX3260750
experiment_title: GSM2806692: CD3/28_24h_1; Mus musculus; RNA-Seq
study_name: GSE104725
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 1500
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 1500
experiment_attribute: GEO Accession: GSM2806692
sample_alias: GSM2806692
sample_accession: SRS2574060
study_alias: GSE104725
study_accession: SRP119595
study_title: Quantitative Transcriptome Analysis of T cells stimulated with STING ligands
study_type: Transcriptome Analysis
center_project_name: GSE104725
submission_accession: SRA617887
submission_comment: submission brokered by GEO
submission_center: GEO
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
source_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

study_abstract:
STING 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: NaÃƒÂ¯ve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.


run_alias: GSM2806686_r1
run_accession: SRR6148724
updated_date: 2017-10-11
experiment_name: GSM2806686
experiment_alias: GSM2806686
experiment_accession: SRX3260744
experiment_title: GSM2806686: Naive CD4_1; Mus musculus; RNA-Seq
study_name: GSE104725
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 1500
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 1500
experiment_attribute: GEO Accession: GSM2806686
sample_alias: GSM2806686
sample_accession: SRS2574058
study_alias: GSE104725
study_accession: SRP119595
study_title: Quantitative Transcriptome Analysis of T cells stimulated with STING ligands
study_type: Transcriptome Analysis
center_project_name: GSE104725
submission_accession: SRA617887
submission_comment: submission brokered by GEO
submission_center: GEO
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
source_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 (naÃƒÂ¯ve)


run_alias: GSM2806924_r1
run_accession: SRR6150415
updated_date: 2017-10-11
experiment_name: GSM2806924
experiment_alias: GSM2806924
experiment_accession: SRX3262427
experiment_title: GSM2806924: ATCC27064; Streptomyces clavuligerus; RNA-Seq
study_name: GSE104738
library_strategy: RNA-Seq
library_source: TRANSCRIPTOMIC
library_selection: cDNA
library_layout: SINGLE -
platform: ILLUMINA
instrument_model: Illumina HiSeq 2000
platform_parameters: INSTRUMENT_MODEL: Illumina HiSeq 2000
experiment_attribute: GEO Accession: GSM2806924
sample_alias: GSM2806924
sample_accession: SRS2575351
study_alias: GSE104738
study_accession: SRP119613
study_type: Transcriptome Analysis
center_project_name: GSE104738
submission_accession: SRA617916
submission_comment: submission brokered by GEO
submission_center: GEO
sradb_updated: 2018-05-10 18:11:11
library_construction_protocol:
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 Ã¢â‚¬ËœTurbo DNA-freeÃ¢â‚¬â„¢ 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 manufacturerÃ¢â‚¬â„¢s instructions (Illumina).

sample_attribute:
source_name: mycelium || phenotype: wildtype || strain: ATCC 27064 || type-material: type strain of Streptomyces clavuligerus

study_title:
The compact genome in the clavulanic acid producing Streptomyces  strain unravels a variety of horizontal transfer reservoirs

study_abstract:
Bacterial 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 sequencing


run_accession: SRR6214059
updated_date: 2017-10-25
experiment_accession: SRX3322822
sample_accession: SRS2627513
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624103
sradb_updated: 2018-05-10 18:11:11
study_abstract:
Summary: 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.

study_attribute:
GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = encode-help@lists.stanford.edu; 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


run_accession: SRR6214060
updated_date: 2017-10-25
experiment_accession: SRX3322823
sample_alias: ENCODE biosample ENCBS195LAY
sample_accession: SRS1860811
description: Homo sapiens MCF-7 immortalized cell line
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624103
sradb_updated: 2018-05-10 18:11:11
sample_url_link:
ENCBS195LAY 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.pdf

sample_attribute:
dev 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

study_abstract:
Summary: 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.

study_attribute:
GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = encode-help@lists.stanford.edu; 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


run_accession: SRR6214107
updated_date: 2017-10-25
experiment_accession: SRX3322868
sample_alias: ENCODE biosample ENCBS200IWR
sample_accession: SRS1860706
description: Homo sapiens MCF-7 immortalized cell line
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624135
sradb_updated: 2018-05-10 18:11:11
sample_url_link:
ENCBS200IWR 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_0031

sample_attribute:
dev 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

study_abstract:
Summary: 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.

study_attribute:
GEO Accession: GSE59395 || Project Contact: Name = ENCODE, DCC; Email = encode-help@lists.stanford.edu; 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


run_accession: SRR6214108
updated_date: 2017-10-25
experiment_accession: SRX3322869
sample_alias: ENCODE biosample ENCBS488MMM
sample_accession: SRS1860859
description: Homo sapiens MCF-7 immortalized cell line
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624135
sradb_updated: 2018-05-10 18:11:11
sample_url_link:
ENCBS488MMM 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_0031

sample_attribute:
dev 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


run_accession: SRR6214195
updated_date: 2017-10-25
experiment_accession: SRX3322942
sample_alias: ENCODE biosample ENCBS609QTY
sample_accession: SRS1860691
description: Homo sapiens MCF-7 immortalized cell line
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624170
sradb_updated: 2018-05-10 18:11:11
sample_url_link:
ENCBS609QTY 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_0031

sample_attribute:
dev 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


run_accession: SRR6214198
updated_date: 2017-10-25
experiment_accession: SRX3322945
sample_alias: ENCODE biosample ENCBS110CZN
sample_accession: SRS1860750
description: Homo sapiens MCF-7 immortalized cell line
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624171
sradb_updated: 2018-05-10 18:11:11
sample_url_link:
ENCBS110CZN 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.pdf


run_accession: SRR6214197
updated_date: 2017-10-25
experiment_accession: SRX3322944
sample_alias: ENCODE biosample ENCBS764AUT
sample_accession: SRS1860751
description: Homo sapiens MCF-7 immortalized cell line
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624171
sradb_updated: 2018-05-10 18:11:11
sample_url_link:
ENCBS764AUT 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.pdf

sample_attribute:
dev 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


run_accession: SRR6214345
updated_date: 2017-10-25
experiment_accession: SRX3323022
sample_alias: ENCODE biosample ENCBS547AXB
sample_accession: SRS1860470
description: Homo sapiens MCF-7 immortalized cell line
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624224
sradb_updated: 2018-05-10 18:11:11
sample_url_link:
ENCBS547AXB 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_0031


run_accession: SRR6214414
updated_date: 2017-10-25
experiment_accession: SRX3323090
sample_alias: ENCODE biosample ENCBS670IYV
sample_accession: SRS1860582
description: Homo sapiens MCF-7 immortalized cell line
study_alias: GSE59395
study_accession: SRP012412
study_title: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_type: Epigenetics
center_project_name: GSE59395: Genome-wide map of regulatory interactions in the human genome
study_url_link: GEO Series GSE59395: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59395
submission_accession: SRA624269
sradb_updated: 2018-05-10 18:11:11
sample_url_link:
ENCBS670IYV 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_0031


run_accession: SRR6240066
updated_date: 2017-10-31
experiment_accession: SRX3347394
sample_alias: P8
sample_accession: SRS2496969
description: synchronous ductal carcinoma in situ
study_alias: PRJNA397565
study_accession: SRP116771
study_title: Synchronous ductal carcinoma in situ single cell DNA sequencing
study_type: Other
center_project_name: Homo sapiens
submission_accession: SRA626821
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
isolate: P8 || age: 62 || biomaterial_provider: Nicholas Navin PhD, 1515 holcombe blvd, Houston TX 77030, S15.8116b BSRB || sex: female || tissue: Breast || disease: DOID:3008 || disease_stage: IIA || sample_type: single cells || BioSampleModel: Human

study_abstract:
Ductal Carcinoma in situ (DCIS) is an early stage breast cancer and nonobligatory precursor to invasive ductal cancer (IDC). Genomic evolution during invasion has been difficult to delineate in bulk tissues due to the limited number of tumor cells in the ducts and the extensive intratumor heterogeneity. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) combining laser-catapulting and single cell DNA sequencing to measure genomic copy number profiles from single tumor cells while preserving their spatial context. We applied TSCS to profile 1075 single cells from 10 synchronous DCIS patients, in addition to deep-exome sequencing of microdissected regions. Our data shows that genomic evolution was intraductal and gave rise to multiple clonal subpopulations that escaped the ducts and expanded to form invasive legions. Our data suggests that invasive clones are pre-programmed in the ducts, at the earliest stages of tumor progression, having implications for diagnostics and treatment of DCIS patients.


run_accession: SRR6269871
updated_date: 2017-11-09
experiment_accession: SRX3375937
sample_alias: P10
sample_accession: SRS2428598
description: synchronous ductal carcinoma in situ
study_alias: PRJNA397565
study_accession: SRP116771
study_title: Synchronous ductal carcinoma in situ single cell DNA sequencing
study_type: Other
center_project_name: Homo sapiens
submission_accession: SRA629574
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
isolate: 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


run_accession: SRR6269856
updated_date: 2017-11-08
experiment_accession: SRX3375952
sample_alias: P5
sample_accession: SRS2493573
description: synchronous ductal carcinoma in situ
study_alias: PRJNA397565
study_accession: SRP116771
study_title: Synchronous ductal carcinoma in situ single cell DNA sequencing
study_type: Other
center_project_name: Homo sapiens
submission_accession: SRA629574
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
isolate: 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


run_accession: SRR6269864
updated_date: 2017-11-09
experiment_accession: SRX3375944
sample_alias: P1
sample_accession: SRS2535762
study_alias: PRJNA397565
study_accession: SRP116771
study_title: Synchronous ductal carcinoma in situ single cell DNA sequencing
study_type: Other
center_project_name: Homo sapiens
submission_accession: SRA629574
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
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


run_accession: SRR6312060
updated_date: 2017-11-22
experiment_accession: SRX3412308
sample_alias: Vaginal swabs
sample_accession: SRS2246411
study_alias: PRJNA388787
study_accession: SRP108425
study_title: Co2 Laser GSM
study_type: Other
center_project_name: Homo sapiens
submission_accession: SRA632651
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
isolate: Human samples || age: >50 || biomaterial_provider: vaginal swab || sex: female || tissue: Vagina || BioSampleModel: Human

study_abstract:
Fractional CO2 Laser for Genitourinary Syndrome of Menopause in breast cancer survivors: clinical, immunological and microbiological aspects


run_accession: SRR6313922
updated_date: 2017-11-24
experiment_accession: SRX3413862
sample_accession: SRS2707044
study_alias: PRJNA358389
study_accession: SRP095725
study_type: Exome Sequencing
center_project_name: Mus musculus strain:C57BL/6N
submission_accession: SRA632956
sradb_updated: 2018-05-10 18:11:11
study_title:
Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinoma

study_abstract:
We 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.


run_accession: SRR6709041
updated_date: 2018-02-12
experiment_accession: SRX3683141
sample_alias: DRS035236
sample_accession: DRS035236
common_name: human
study_accession: SRP132698
submission_accession: SRA658713
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
description: 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


run_accession: SRR6749583
updated_date: 2018-02-20
experiment_accession: SRX3722246
sample_alias: T47D
sample_accession: SRS1359716
study_accession: SRP133088
submission_accession: SRA660374
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
isolate: T47D breast cancer cells || age: NA || biomaterial_provider: Myles Brown || sex: not determined || tissue: breast cancer || cell_line: T47D || BioSampleModel: Human


run_accession: SRR6781939
updated_date: 2018-02-26
experiment_accession: SRX3741800
sample_alias: BCSC-LCM
sample_accession: SRS2123144
study_accession: SRP103895
submission_accession: SRA662102
sradb_updated: 2018-05-10 18:11:11
sample_attribute:
isolate: a breast cancer patient || age: 92 || biomaterial_provider: Henrik Ditzel || sex: female || tissue: breast || BioSampleModel: Human


run_accession: SRR6920746
updated_date: 2018-03-30
experiment_accession: SRX3868135
sample_accession: SRS3042212
study_alias: 145181
study_accession: SRP015682
study_title: Poecilia formosa strain:female Genome sequencing and assembly
study_type: Whole Genome Sequencing
center_project_name: Poecilia formosa strain:female
submission_accession: SRA677792
sradb_updated: 2018-05-10 18:11:11
study_abstract:
The 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.


