rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
59850,SRR12045008,SRX8573978,SRS6865977,SRP267842,PRJNA640350,Bulk RNA seq data to assess an improved zebrafish transcriptome annotation,GSE152759,Transcriptome Analysis,oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS,,pubmed:32831172,,Nr2f2andY1 positive rep3,GSM4625929,,tissue:venous endothelial cells|Stage:38 hpf isolated cells,Nr2f2andY1 positive rep3,Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples  if index sequences were non redundant  we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95  RefSeq GCF 000002035.6  or a custom annotation V4.3.gtf  included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation,venous endothelial cells,embryos were dissociated into single cell suspensions  immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,,Stage:38 hpf isolated cells,GSM4625929,GSM4625929: Nr2f2andY1 positive rep3; Danio rerio; RNA Seq,GSM4625929,,1,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,GEO Accession:GSM4625929,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP267842,,,Nr2f2_y1_WT3.R1.fastq Nr2f2_y1_WT3.R2.fastq,fastq fastq,4563696700.0,45636967.0,GSM4625929 r1,0:50 1:50,A:1065004679;C:1130434821;G:1255426694;T:1110932954;N:1897552,50,50,,,1065004679,1130434821,1255426694,1110932954,1897552,SRX8573978,SRS6865977,SRA1088645,GEO,"Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School",2,0.82873,0.84247,0.30011,0.31275,0.76952,0.7713,0.70461,0.5211,50,50,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,smarter,bulk,bulk,bulk,,United States,2020-06-18,Pharyngula,Embryo,Endothelium,Cardiovascular System
59851,SRR12045007,SRX8573977,SRS6865975,SRP267842,PRJNA640350,Bulk RNA seq data to assess an improved zebrafish transcriptome annotation,GSE152759,Transcriptome Analysis,oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS,,pubmed:32831172,,Nr2f2andY1 positive rep2,GSM4625928,,tissue:venous endothelial cells|Stage:38 hpf isolated cells,Nr2f2andY1 positive rep2,Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples  if index sequences were non redundant  we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95  RefSeq GCF 000002035.6  or a custom annotation V4.3.gtf  included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation,venous endothelial cells,embryos were dissociated into single cell suspensions  immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,,Stage:38 hpf isolated cells,GSM4625928,GSM4625928: Nr2f2andY1 positive rep2; Danio rerio; RNA Seq,GSM4625928,,1,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,GEO Accession:GSM4625928,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP267842,,,Nr2f2_y1_WT2.R1.fastq Nr2f2_y1_WT2.R2.fastq,fastq fastq,5035288300.0,50352883.0,GSM4625928 r1,0:50 1:50,A:1193841347;C:1228803073;G:1365132247;T:1245428530;N:2083103,50,50,,,1193841347,1228803073,1365132247,1245428530,2083103,SRX8573977,SRS6865975,SRA1088645,GEO,"Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School",2,0.81964,0.83355,0.31676,0.32935,0.77394,0.77179,0.69865,0.54887,50,50,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,smarter,bulk,bulk,bulk,,United States,2020-06-18,Pharyngula,Embryo,Endothelium,Cardiovascular System
59852,SRR12045006,SRX8573976,SRS6865974,SRP267842,PRJNA640350,Bulk RNA seq data to assess an improved zebrafish transcriptome annotation,GSE152759,Transcriptome Analysis,oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS,,pubmed:32831172,,Nr2f2andY1 positive rep1,GSM4625927,,tissue:venous endothelial cells|Stage:38 hpf isolated cells,Nr2f2andY1 positive rep1,Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples  if index sequences were non redundant  we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95  RefSeq GCF 000002035.6  or a custom annotation V4.3.gtf  included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation,venous endothelial cells,embryos were dissociated into single cell suspensions  immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,,Stage:38 hpf isolated cells,GSM4625927,GSM4625927: Nr2f2andY1 positive rep1; Danio rerio; RNA Seq,GSM4625927,,1,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,GEO Accession:GSM4625927,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP267842,,,Nr2f2_y1_WT1.R1.fastq Nr2f2_y1_WT1.R2.fastq,fastq fastq,4790242000.0,47902420.0,GSM4625927 r1,0:50 1:50,A:1058654389;C:1248085905;G:1387245634;T:1094388168;N:1867904,50,50,,,1058654389,1248085905,1387245634,1094388168,1867904,SRX8573976,SRS6865974,SRA1088645,GEO,"Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School",2,0.83369,0.84436,0.23642,0.24601,0.77788,0.77977,0.73738,0.55719,50,50,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,smarter,bulk,bulk,bulk,,United States,2020-06-18,Pharyngula,Embryo,Endothelium,Cardiovascular System