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
47897,SRR6908713,SRX3856801,SRS3100393,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 lymphocytes,GSM3070139,,tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM6 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070139,GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq,GSM3070139,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_lymphocytes_L001_R1_001.fastq.gz WKM6_lymphocytes_L001_R2_001.fastq.gz,fastq fastq,1092718271.0,7238113.0,GSM3070139 r1,0:75.49 1:75.48,A:308417237;C:162459915;G:183666585;T:438104581;N:69953,75,75,,,308417237,162459915,183666585,438104581,69953,SRX3856801,SRS3100393,SRA675960,GEO,Hubrecht Institute,2,0.33032,0.81969,0.25647,0.49446,0.98587,0.93105,0.47765,0.53939,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47898,SRR6908714,SRX3856801,SRS3100393,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 lymphocytes,GSM3070139,,tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM6 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070139,GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq,GSM3070139,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_lymphocytes_L002_R1_001.fastq.gz WKM6_lymphocytes_L002_R2_001.fastq.gz,fastq fastq,988686695.0,6550079.0,GSM3070139 r2,0:75.49 1:75.46,A:281384679;C:146335731;G:165878017;T:395040397;N:47871,75,75,,,281384679,146335731,165878017,395040397,47871,SRX3856801,SRS3100393,SRA675960,GEO,Hubrecht Institute,2,0.31311,0.79325,0.23663,0.48843,0.99034,0.95471,0.47178,0.54622,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47899,SRR6908715,SRX3856801,SRS3100393,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 lymphocytes,GSM3070139,,tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM6 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070139,GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq,GSM3070139,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_lymphocytes_L003_R1_001.fastq.gz WKM6_lymphocytes_L003_R2_001.fastq.gz,fastq fastq,965970467.0,6397966.0,GSM3070139 r3,0:75.51 1:75.47,A:271037832;C:143188198;G:162584210;T:389145889;N:14338,75,75,,,271037832,143188198,162584210,389145889,14338,SRX3856801,SRS3100393,SRA675960,GEO,Hubrecht Institute,2,0.2983,0.81397,0.23255,0.49479,0.99377,0.94379,0.43187,0.54702,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47900,SRR6908716,SRX3856801,SRS3100393,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 lymphocytes,GSM3070139,,tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM6 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070139,GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq,GSM3070139,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_lymphocytes_L004_R1_001.fastq.gz WKM6_lymphocytes_L004_R2_001.fastq.gz,fastq fastq,845107841.0,5598430.0,GSM3070139 r4,0:75.50 1:75.46,A:239787549;C:124312776;G:144002735;T:336997076;N:7705,75,75,,,239787549,124312776,144002735,336997076,7705,SRX3856801,SRS3100393,SRA675960,GEO,Hubrecht Institute,2,0.27606,0.8077,0.21352,0.49895,0.99502,0.95511,0.37654,0.5537,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47905,SRR6908705,SRX3856799,SRS3100391,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 lymphocytes,GSM3070137,,tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM5 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070137,GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq,GSM3070137,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_lymphocytes_L001_R1_001.fastq.gz WKM5_lymphocytes_L001_R2_001.fastq.gz,fastq fastq,989705998.0,6559370.0,GSM3070137 r1,0:75.45 1:75.43,A:297302138;C:149495824;G:174348330;T:368343979;N:215727,75,75,,,297302138,149495824,174348330,368343979,215727,SRX3856799,SRS3100391,SRA675960,GEO,Hubrecht Institute,2,0.24742,0.6658,0.20828,0.41062,0.98214,0.85423,0.46204,0.47999,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47906,SRR6908706,SRX3856799,SRS3100391,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 lymphocytes,GSM3070137,,tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM5 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070137,GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq,GSM3070137,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_lymphocytes_L002_R1_001.fastq.gz WKM5_lymphocytes_L002_R2_001.fastq.gz,fastq fastq,966752947.0,6406981.0,GSM3070137 r2,0:75.44 1:75.45,A:289601664;C:144620642;G:173993992;T:358339663;N:196986,75,75,,,289601664,144620642,173993992,358339663,196986,SRX3856799,SRS3100391,SRA675960,GEO,Hubrecht Institute,2,0.23604,0.65405,0.20033,0.39718,0.98196,0.8636,0.50139,0.50729,74,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47907,SRR6908707,SRX3856799,SRS3100391,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 lymphocytes,GSM3070137,,tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM5 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070137,GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq,GSM3070137,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_lymphocytes_L003_R1_001.fastq.gz WKM5_lymphocytes_L003_R2_001.fastq.gz,fastq fastq,958861430.0,6354224.0,GSM3070137 r3,0:75.46 1:75.44,A:286188763;C:145686623;G:169054587;T:357878024;N:53433,75,75,,,286188763,145686623,169054587,357878024,53433,SRX3856799,SRS3100391,SRA675960,GEO,Hubrecht Institute,2,0.25215,0.67286,0.20951,0.41571,0.98707,0.84611,0.45707,0.51523,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47908,SRR6908708,SRX3856799,SRS3100391,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 lymphocytes,GSM3070137,,tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM5 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070137,GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq,GSM3070137,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_lymphocytes_L004_R2_001.fastq.gz WKM5_lymphocytes_L004_R1_001.fastq.gz,fastq fastq,907053718.0,6010618.0,GSM3070137 r4,0:75.45 1:75.46,A:270238988;C:137187310;G:162483694;T:337104230;N:39496,75,75,,,270238988,137187310,162483694,337104230,39496,SRX3856799,SRS3100391,SRA675960,GEO,Hubrecht Institute,2,0.2382,0.66089,0.20055,0.40225,0.98537,0.86109,0.4862,0.51182,75,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47953,SRR6908655,SRX3856786,SRS3100377,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 lymphocytes,GSM3070125,,tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM10 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070125,GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq,GSM3070125,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070125,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_lymphocytes_L001_R1_001.fastq.gz WKM10_lymphocytes_L001_R2_001.fastq.gz,fastq fastq,1505229869.0,9975689.0,GSM3070125 r1,0:75.46 1:75.43,A:446863117;C:223332557;G:257023910;T:577686078;N:324207,75,75,,,446863117,223332557,257023910,577686078,324207,SRX3856786,SRS3100377,SRA675960,GEO,Hubrecht Institute,2,0.27651,0.70172,0.22976,0.41642,0.98198,0.85401,0.46672,0.52056,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47954,SRR6908656,SRX3856786,SRS3100377,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 lymphocytes,GSM3070125,,tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM10 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070125,GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq,GSM3070125,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070125,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_lymphocytes_L002_R1_001.fastq.gz WKM10_lymphocytes_L002_R2_001.fastq.gz,fastq fastq,1466970503.0,9721974.0,GSM3070125 r2,0:75.45 1:75.44,A:434939637;C:215624726;G:255310153;T:560791208;N:304779,75,75,,,434939637,215624726,255310153,560791208,304779,SRX3856786,SRS3100377,SRA675960,GEO,Hubrecht Institute,2,0.263,0.6934,0.21939,0.4057,0.98127,0.86417,0.4805,0.49132,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47955,SRR6908657,SRX3856786,SRS3100377,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 lymphocytes,GSM3070125,,tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM10 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070125,GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq,GSM3070125,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070125,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_lymphocytes_L003_R2_001.fastq.gz WKM10_lymphocytes_L003_R1_001.fastq.gz,fastq fastq,1456610152.0,9652493.0,GSM3070125 r3,0:75.46 1:75.44,A:429303329;C:217559734;G:249207876;T:560459433;N:79780,75,75,,,429303329,217559734,249207876,560459433,79780,SRX3856786,SRS3100377,SRA675960,GEO,Hubrecht Institute,2,0.28238,0.70747,0.2323,0.4212,0.98683,0.84575,0.43386,0.5155,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47956,SRR6908658,SRX3856786,SRS3100377,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 lymphocytes,GSM3070125,,tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM10 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070125,GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq,GSM3070125,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070125,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_lymphocytes_L004_R1_001.fastq.gz WKM10_lymphocytes_L004_R2_001.fastq.gz,fastq fastq,1372270103.0,9093444.0,GSM3070125 r4,0:75.46 1:75.45,A:404750065;C:203942354;G:237441524;T:526077075;N:59085,75,75,,,404750065,203942354,237441524,526077075,59085,SRX3856786,SRS3100377,SRA675960,GEO,Hubrecht Institute,2,0.2714,0.69516,0.22843,0.40836,0.98602,0.8607,0.47846,0.52284,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
51245,SRR8599806,SRX5399821,SRS4386664,SRP186433,PRJNA523477,The alternative splicing regulator Nova2 constrains vascular Erk signalling to limit specification of the lymphatic lineage,PRJNA523477,Other,The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre existing veins post venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors  however the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature  expanded and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing  Nova2. In zebrafish and human endothelial cells  Nova2 selectively regulates pre mRNA splicing for components of signalling pathways and phosphoproteins. Nova2 deficient endothelial cells display increased Mapk/Erk signalling and Prox1 expression is dynamically controlled by Erk signalling. We identify a mechanism whereby Nova2 regulated splicing constrains Erk signalling  thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.,,,,mut1 S5 R1,mut1 S5 R1,,isolate:mut FACS1|age:N/A|sex:N/A|tissue:lymphatic|BioSampleModel:Model organism or animal,,,,,,,,,mut1 S5 R1 Danio rerio,mut1 S5 R1,mut1 S5 R1,mut1 S5 R1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP186433,,,mut1_S5_R1_001.fastq.gz mut1_S5_R2_001.fastq.gz,fastq fastq,9837663895.0,65246962.0,mut1 S5 R1 001.fastq.gz,0:75.39 1:75.39,A:2510672978;C:2396748014;G:2421271907;T:2502051457;N:6919539,75,75,,,2510672978,2396748014,2421271907,2502051457,6919539,SRX5399821,SRS4386664,SRA851016,Salk Institute|Salk,Salk Institute,2,0.9223,0.92439,0.04802,0.04707,0.72604,0.73292,0.46138,0.44694,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-02-23,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
51246,SRR8599807,SRX5399820,SRS4386663,SRP186433,PRJNA523477,The alternative splicing regulator Nova2 constrains vascular Erk signalling to limit specification of the lymphatic lineage,PRJNA523477,Other,The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre existing veins post venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors  however the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature  expanded and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing  Nova2. In zebrafish and human endothelial cells  Nova2 selectively regulates pre mRNA splicing for components of signalling pathways and phosphoproteins. Nova2 deficient endothelial cells display increased Mapk/Erk signalling and Prox1 expression is dynamically controlled by Erk signalling. We identify a mechanism whereby Nova2 regulated splicing constrains Erk signalling  thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.,,,,mut2 S6 R1,mut2 S6 R1,,isolate:mut FACS2|age:N/A|sex:N/A|tissue:lymphatic|BioSampleModel:Model organism or animal,,,,,,,,,mut2 S6 R1 Danio rerio,mut2 S6 R1,mut2 S6 R1,mut2 S6 R1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP186433,,,mut2_S6_R1_001.fastq.gz mut2_S6_R2_001.fastq.gz,fastq fastq,9533271942.0,63195057.0,mut2 S6 R1 001.fastq.gz,0:75.46 1:75.40,A:2433373292;C:2316742432;G:2363052055;T:2416454490;N:3649673,75,75,,,2433373292,2316742432,2363052055,2416454490,3649673,SRX5399820,SRS4386663,SRA851016,Salk Institute|Salk,Salk Institute,2,0.92764,0.93036,0.05365,0.05151,0.73036,0.73805,0.46895,0.46735,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-02-23,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
51247,SRR8599808,SRX5399819,SRS4386662,SRP186433,PRJNA523477,The alternative splicing regulator Nova2 constrains vascular Erk signalling to limit specification of the lymphatic lineage,PRJNA523477,Other,The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre existing veins post venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors  however the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature  expanded and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing  Nova2. In zebrafish and human endothelial cells  Nova2 selectively regulates pre mRNA splicing for components of signalling pathways and phosphoproteins. Nova2 deficient endothelial cells display increased Mapk/Erk signalling and Prox1 expression is dynamically controlled by Erk signalling. We identify a mechanism whereby Nova2 regulated splicing constrains Erk signalling  thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.,,,,mut3 S7 R1,mut3 S7 R1,,isolate:mut FACS3|age:N/A|sex:N/A|tissue:lymphatic|BioSampleModel:Model organism or animal,,,,,,,,,mut3 S7 R1 Danio rerio,mut3 S7 R1,mut3 S7 R1,mut3 S7 R1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP186433,,,mut3_S7_R1_001.fastq.gz mut3_S7_R2_001.fastq.gz,fastq fastq,9615872706.0,63753352.0,mut3 S7 R1 001.fastq.gz,0:75.44 1:75.39,A:2467603664;C:2330407989;G:2360302038;T:2453101697;N:4457318,75,75,,,2467603664,2330407989,2360302038,2453101697,4457318,SRX5399819,SRS4386662,SRA851016,Salk Institute|Salk,Salk Institute,2,0.91265,0.91612,0.04903,0.04678,0.72912,0.73519,0.46861,0.46542,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-02-23,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
51248,SRR8599809,SRX5399818,SRS4386661,SRP186433,PRJNA523477,The alternative splicing regulator Nova2 constrains vascular Erk signalling to limit specification of the lymphatic lineage,PRJNA523477,Other,The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre existing veins post venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors  however the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature  expanded and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing  Nova2. In zebrafish and human endothelial cells  Nova2 selectively regulates pre mRNA splicing for components of signalling pathways and phosphoproteins. Nova2 deficient endothelial cells display increased Mapk/Erk signalling and Prox1 expression is dynamically controlled by Erk signalling. We identify a mechanism whereby Nova2 regulated splicing constrains Erk signalling  thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.,,,,mut4 S8 R1,mut4 S8 R1,,isolate:mut FACS4|age:N/A|sex:N/A|tissue:lymphatic|BioSampleModel:Model organism or animal,,,,,,,,,mut4 S8 R1 Danio rerio,mut4 S8 R1,mut4 S8 R1,mut4 S8 R1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP186433,,,mut4_S8_R1_001.fastq.gz mut4_S8_R2_001.fastq.gz,fastq fastq,9628016681.0,63857361.0,mut4 S8 R1 001.fastq.gz,0:75.38 1:75.39,A:2461125050;C:2342156353;G:2366792825;T:2450529037;N:7413416,75,75,,,2461125050,2342156353,2366792825,2450529037,7413416,SRX5399818,SRS4386661,SRA851016,Salk Institute|Salk,Salk Institute,2,0.92833,0.93039,0.04845,0.04626,0.72504,0.73107,0.46741,0.46043,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-02-23,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
51249,SRR8599810,SRX5399817,SRS4386660,SRP186433,PRJNA523477,The alternative splicing regulator Nova2 constrains vascular Erk signalling to limit specification of the lymphatic lineage,PRJNA523477,Other,The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre existing veins post venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors  however the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature  expanded and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing  Nova2. In zebrafish and human endothelial cells  Nova2 selectively regulates pre mRNA splicing for components of signalling pathways and phosphoproteins. Nova2 deficient endothelial cells display increased Mapk/Erk signalling and Prox1 expression is dynamically controlled by Erk signalling. We identify a mechanism whereby Nova2 regulated splicing constrains Erk signalling  thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.,,,,sib1 S1 R1,sib1 S1 R1,,isolate:sib FACS1|age:N/A|sex:N/A|tissue:lymphatic|BioSampleModel:Model organism or animal,,,,,,,,,sib1 S1 R1 Danio  rerio,sib1 S1 R1,sib1 S1 R1,sib1 S1 R1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP186433,,,sib1_S1_R1_001.fastq.gz sib1_S1_R2_001.fastq.gz,fastq fastq,8260538032.0,54746632.0,sib1 S1 R1 001.fastq.gz,0:75.48 1:75.41,A:2109874601;C:2016630266;G:2030604420;T:2100518772;N:2909973,75,75,,,2109874601,2016630266,2030604420,2100518772,2909973,SRX5399817,SRS4386660,SRA851016,Salk Institute|Salk,Salk Institute,2,0.9274,0.93049,0.04415,0.04306,0.72819,0.73397,0.45755,0.4619,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-02-23,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
51250,SRR8599811,SRX5399816,SRS4386657,SRP186433,PRJNA523477,The alternative splicing regulator Nova2 constrains vascular Erk signalling to limit specification of the lymphatic lineage,PRJNA523477,Other,The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre existing veins post venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors  however the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature  expanded and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing  Nova2. In zebrafish and human endothelial cells  Nova2 selectively regulates pre mRNA splicing for components of signalling pathways and phosphoproteins. Nova2 deficient endothelial cells display increased Mapk/Erk signalling and Prox1 expression is dynamically controlled by Erk signalling. We identify a mechanism whereby Nova2 regulated splicing constrains Erk signalling  thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.,,,,sib2 S2 R1,sib2 S2 R1,,isolate:sib FACS2|age:N/A|sex:N/A|tissue:lymphatic|BioSampleModel:Model organism or animal,,,,,,,,,sib2 S2 R1 Danio rerio,sib2 S2 R1,sib2 S2 R1,sib2 S2 R1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP186433,,,sib2_S2_R2_001.fastq.gz sib2_S2_R1_001.fastq.gz,fastq fastq,9696189954.0,64289000.0,sib2 S2 R1 001.fastq.gz,0:75.43 1:75.39,A:2490621064;C:2347396873;G:2379070189;T:2474275949;N:4825879,75,75,,,2490621064,2347396873,2379070189,2474275949,4825879,SRX5399816,SRS4386657,SRA851016,Salk Institute|Salk,Salk Institute,2,0.92625,0.92998,0.04931,0.04808,0.72819,0.73529,0.4694,0.46291,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-02-23,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
51251,SRR8599812,SRX5399815,SRS4386658,SRP186433,PRJNA523477,The alternative splicing regulator Nova2 constrains vascular Erk signalling to limit specification of the lymphatic lineage,PRJNA523477,Other,The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre existing veins post venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors  however the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature  expanded and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing  Nova2. In zebrafish and human endothelial cells  Nova2 selectively regulates pre mRNA splicing for components of signalling pathways and phosphoproteins. Nova2 deficient endothelial cells display increased Mapk/Erk signalling and Prox1 expression is dynamically controlled by Erk signalling. We identify a mechanism whereby Nova2 regulated splicing constrains Erk signalling  thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.,,,,sib3 S3 R1,sib3 S3 R1,,isolate:sib FACS3|age:N/A|sex:N/A|tissue:lymphatic|BioSampleModel:Model organism or animal,,,,,,,,,sib3 S3 R1 Danio rerio,sib3 S3 R1,sib3 S3 R1,sib3 S3 R1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP186433,,,sib3_S3_R1_001.fastq.gz sib3_S3_R2_001.fastq.gz,fastq fastq,8880743673.0,58911690.0,sib3 S3 R1 001.fastq.gz,0:75.38 1:75.37,A:2285629820;C:2145183448;G:2171941009;T:2271950133;N:6039263,75,75,,,2285629820,2145183448,2171941009,2271950133,6039263,SRX5399815,SRS4386658,SRA851016,Salk Institute|Salk,Salk Institute,2,0.9287,0.93205,0.04916,0.04823,0.71587,0.72407,0.46907,0.45474,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-02-23,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
51252,SRR8599813,SRX5399814,SRS4386659,SRP186433,PRJNA523477,The alternative splicing regulator Nova2 constrains vascular Erk signalling to limit specification of the lymphatic lineage,PRJNA523477,Other,The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre existing veins post venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors  however the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature  expanded and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing  Nova2. In zebrafish and human endothelial cells  Nova2 selectively regulates pre mRNA splicing for components of signalling pathways and phosphoproteins. Nova2 deficient endothelial cells display increased Mapk/Erk signalling and Prox1 expression is dynamically controlled by Erk signalling. We identify a mechanism whereby Nova2 regulated splicing constrains Erk signalling  thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.,,,,sib4 S4 R1,sib4 S4 R1,,isolate:sib FACS4|age:N/A|sex:N/A|tissue:lymphatic|BioSampleModel:Model organism or animal,,,,,,,,,sib4 S4 R1 Danio rerio,sib4 S4 R1,sib4 S4 R1,sib4 S4 R1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP186433,,,sib4_S4_R1_001.fastq.gz sib4_S4_R2_001.fastq.gz,fastq fastq,9675337111.0,64177351.0,sib4 S4 R1 001.fastq.gz,0:75.38 1:75.38,A:2488819595;C:2338829695;G:2368389781;T:2472515294;N:6782746,75,75,,,2488819595,2338829695,2368389781,2472515294,6782746,SRX5399814,SRS4386659,SRA851016,Salk Institute|Salk,Salk Institute,2,0.9214,0.92359,0.04736,0.04551,0.72563,0.73135,0.46669,0.4723,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-02-23,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68437,SRR17745565,SRX13908047,SRS11764646,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Propy 1uM Lymph TCGACGTC TAAGGCTC,GSM5835390,,tissue:TCGACGTC TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Propy 1uM Lymph TCGACGTC TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,TCGACGTC TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835390,GSM5835390: TNBS Propy 1uM Lymph TCGACGTC TAAGGCTC; Danio rerio; RNA Seq,GSM5835390 r1,GSM5835390,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,TCGACGTC_TAAGGCTC.1.fastq.gz TCGACGTC_TAAGGCTC.2.fastq.gz,fastq fastq,1922496.0,25296.0,GSM5835390 r1,0:38 1:38,A:171435;C:632667;G:900479;T:217189;N:726,38,38,,,171435,632667,900479,217189,726,SRX13908047,SRS11764646,,,Brigham and Women's Hospital,2,0.25357,0.30242,0.2361,0.28402,0.99707,0.99738,0.49729,0.6149,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68438,SRR17745566,SRX13908046,SRS11764648,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Propy 1uM Lymph TGCAGCTA TAAGGCTC,GSM5835389,,tissue:TGCAGCTA TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Propy 1uM Lymph TGCAGCTA TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,TGCAGCTA TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835389,GSM5835389: TNBS Propy 1uM Lymph TGCAGCTA TAAGGCTC; Danio rerio; RNA Seq,GSM5835389 r1,GSM5835389,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,TGCAGCTA_TAAGGCTC.1.fastq.gz TGCAGCTA_TAAGGCTC.2.fastq.gz,fastq fastq,5085388.0,66913.0,GSM5835389 r1,0:38 1:38,A:622340;C:1663583;G:2030489;T:767902;N:1074,38,38,,,622340,1663583,2030489,767902,1074,SRX13908046,SRS11764648,,,Brigham and Women's Hospital,2,0.39042,0.43673,0.36948,0.41439,0.9893,0.98961,0.49095,0.51432,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68439,SRR17745567,SRX13908045,SRS11764645,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Propy 1uM Lymph CGATCAGT TAAGGCTC,GSM5835388,,tissue:CGATCAGT TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Propy 1uM Lymph CGATCAGT TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,CGATCAGT TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835388,GSM5835388: TNBS Propy 1uM Lymph CGATCAGT TAAGGCTC; Danio rerio; RNA Seq,GSM5835388 r1,GSM5835388,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,CGATCAGT_TAAGGCTC.1.fastq.gz CGATCAGT_TAAGGCTC.2.fastq.gz,fastq fastq,10702244.0,140819.0,GSM5835388 r1,0:38 1:38,A:1426640;C:3419621;G:4146287;T:1706761;N:2935,38,38,,,1426640,3419621,4146287,1706761,2935,SRX13908045,SRS11764645,,,Brigham and Women's Hospital,2,0.48057,0.5245,0.45699,0.49986,0.97506,0.97573,0.50679,0.53345,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68440,SRR17745568,SRX13908044,SRS11764644,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Propy 1uM Lymph CCTAAGAC TAAGGCTC,GSM5835387,,tissue:CCTAAGAC TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Propy 1uM Lymph CCTAAGAC TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,CCTAAGAC TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835387,GSM5835387: TNBS Propy 1uM Lymph CCTAAGAC TAAGGCTC; Danio rerio; RNA Seq,GSM5835387 r1,GSM5835387,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,CCTAAGAC_TAAGGCTC.1.fastq.gz CCTAAGAC_TAAGGCTC.2.fastq.gz,fastq fastq,8838648.0,116298.0,GSM5835387 r1,0:38 1:38,A:1304980;C:2747399;G:3266877;T:1517303;N:2089,38,38,,,1304980,2747399,3266877,1517303,2089,SRX13908044,SRS11764644,,,Brigham and Women's Hospital,2,0.4173,0.45488,0.39377,0.43028,0.97889,0.98023,0.50538,0.50887,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68441,SRR17745569,SRX13908043,SRS11764643,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Propy 20uM Lymph ACTGAGCG TAAGGCTC,GSM5835386,,tissue:ACTGAGCG TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Propy 20uM Lymph ACTGAGCG TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,ACTGAGCG TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835386,GSM5835386: TNBS Propy 20uM Lymph ACTGAGCG TAAGGCTC; Danio rerio; RNA Seq,GSM5835386 r1,GSM5835386,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,ACTGAGCG_TAAGGCTC.1.fastq.gz ACTGAGCG_TAAGGCTC.2.fastq.gz,fastq fastq,4537884.0,59709.0,GSM5835386 r1,0:38 1:38,A:588708;C:1437924;G:1816330;T:694228;N:694,38,38,,,588708,1437924,1816330,694228,694,SRX13908043,SRS11764643,,,Brigham and Women's Hospital,2,0.51374,0.57242,0.48516,0.54139,0.98668,0.98681,0.48986,0.54176,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68442,SRR17745570,SRX13908042,SRS11764642,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Propy 20uM Lymph TAGCGCTC TAAGGCTC,GSM5835385,,tissue:TAGCGCTC TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Propy 20uM Lymph TAGCGCTC TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,TAGCGCTC TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835385,GSM5835385: TNBS Propy 20uM Lymph TAGCGCTC TAAGGCTC; Danio rerio; RNA Seq,GSM5835385 r1,GSM5835385,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,TAGCGCTC_TAAGGCTC.1.fastq.gz TAGCGCTC_TAAGGCTC.2.fastq.gz,fastq fastq,11488464.0,151164.0,GSM5835385 r1,0:38 1:38,A:1767269;C:3587214;G:4096781;T:2034465;N:2735,38,38,,,1767269,3587214,4096781,2034465,2735,SRX13908042,SRS11764642,,,Brigham and Women's Hospital,2,0.60429,0.65879,0.58213,0.63504,0.97106,0.9722,0.52838,0.52136,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68443,SRR17745571,SRX13908041,SRS11764641,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Propy 20uM Lymph ATGCGCAG TAAGGCTC,GSM5835384,,tissue:ATGCGCAG TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Propy 20uM Lymph ATGCGCAG TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,ATGCGCAG TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835384,GSM5835384: TNBS Propy 20uM Lymph ATGCGCAG TAAGGCTC; Danio rerio; RNA Seq,GSM5835384 r1,GSM5835384,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,ATGCGCAG_TAAGGCTC.1.fastq.gz ATGCGCAG_TAAGGCTC.2.fastq.gz,fastq fastq,7090344.0,93294.0,GSM5835384 r1,0:38 1:38,A:1240553;C:2075838;G:2377327;T:1394885;N:1741,38,38,,,1240553,2075838,2377327,1394885,1741,SRX13908041,SRS11764641,,,Brigham and Women's Hospital,2,0.66346,0.7234,0.62974,0.68806,0.96976,0.97179,0.53664,0.54761,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68444,SRR17745572,SRX13908040,SRS11764640,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Propy 20uM Lymph TACGCTGC TAAGGCTC,GSM5835383,,tissue:TACGCTGC TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Propy 20uM Lymph TACGCTGC TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,TACGCTGC TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835383,GSM5835383: TNBS Propy 20uM Lymph TACGCTGC TAAGGCTC; Danio rerio; RNA Seq,GSM5835383 r1,GSM5835383,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,TACGCTGC_TAAGGCTC.1.fastq.gz TACGCTGC_TAAGGCTC.2.fastq.gz,fastq fastq,3458532.0,45507.0,GSM5835383 r1,0:38 1:38,A:476081;C:1074006;G:1355907;T:551309;N:1229,38,38,,,476081,1074006,1355907,551309,1229,SRX13908040,SRS11764640,,,Brigham and Women's Hospital,2,0.56537,0.61783,0.53227,0.58362,0.98687,0.98737,0.5162,0.53056,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68445,SRR17745573,SRX13908039,SRS11764639,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Control 0uM Lymph CGGAGCCT TAAGGCTC,GSM5835382,,tissue:CGGAGCCT TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Control 0uM Lymph CGGAGCCT TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,CGGAGCCT TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835382,GSM5835382: TNBS Control 0uM Lymph CGGAGCCT TAAGGCTC; Danio rerio; RNA Seq,GSM5835382 r1,GSM5835382,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,CGGAGCCT_TAAGGCTC.1.fastq.gz CGGAGCCT_TAAGGCTC.2.fastq.gz,fastq fastq,11976840.0,157590.0,GSM5835382 r1,0:38 1:38,A:1632217;C:3813048;G:4594044;T:1934675;N:2856,38,38,,,1632217,3813048,4594044,1934675,2856,SRX13908039,SRS11764639,,,Brigham and Women's Hospital,2,0.4935,0.54216,0.46695,0.5131,0.96956,0.96992,0.52037,0.51303,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68446,SRR17745574,SRX13908038,SRS11764638,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Control 0uM Lymph GCGTAGTA TAAGGCTC,GSM5835381,,tissue:GCGTAGTA TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Control 0uM Lymph GCGTAGTA TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,GCGTAGTA TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835381,GSM5835381: TNBS Control 0uM Lymph GCGTAGTA TAAGGCTC; Danio rerio; RNA Seq,GSM5835381 r1,GSM5835381,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,GCGTAGTA_TAAGGCTC.1.fastq.gz GCGTAGTA_TAAGGCTC.2.fastq.gz,fastq fastq,2822564.0,37139.0,GSM5835381 r1,0:38 1:38,A:395578;C:865248;G:1112008;T:449031;N:699,38,38,,,395578,865248,1112008,449031,699,SRX13908038,SRS11764638,,,Brigham and Women's Hospital,2,0.44934,0.4965,0.41789,0.46462,0.98965,0.99062,0.53706,0.56101,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68447,SRR17745575,SRX13908037,SRS11764637,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Control 0uM Lymph GGAGCTAC TAAGGCTC,GSM5835380,,tissue:GGAGCTAC TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Control 0uM Lymph GGAGCTAC TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,GGAGCTAC TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835380,GSM5835380: TNBS Control 0uM Lymph GGAGCTAC TAAGGCTC; Danio rerio; RNA Seq,GSM5835380 r1,GSM5835380,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,GGAGCTAC_TAAGGCTC.1.fastq.gz GGAGCTAC_TAAGGCTC.2.fastq.gz,fastq fastq,10063920.0,132420.0,GSM5835380 r1,0:38 1:38,A:1599379;C:3100848;G:3548819;T:1812148;N:2726,38,38,,,1599379,3100848,3548819,1812148,2726,SRX13908037,SRS11764637,,,Brigham and Women's Hospital,2,0.65031,0.69057,0.62414,0.66232,0.96775,0.96855,0.50155,0.52938,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68448,SRR17745576,SRX13908036,SRS11764636,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,TNBS Control 0uM Lymph ACTCGCTA TAAGGCTC,GSM5835379,,tissue:ACTCGCTA TAAGGCTC|strain:AB|Sex:NA|age:NA,TNBS Control 0uM Lymph ACTCGCTA TAAGGCTC,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,ACTCGCTA TAAGGCTC,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835379,GSM5835379: TNBS Control 0uM Lymph ACTCGCTA TAAGGCTC; Danio rerio; RNA Seq,GSM5835379 r1,GSM5835379,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,ACTCGCTA_TAAGGCTC.1.fastq.gz ACTCGCTA_TAAGGCTC.2.fastq.gz,fastq fastq,3572456.0,47006.0,GSM5835379 r1,0:38 1:38,A:633879;C:1031212;G:1219194;T:687126;N:1045,38,38,,,633879,1031212,1219194,687126,1045,SRX13908036,SRS11764636,,,Brigham and Women's Hospital,2,0.41161,0.43665,0.38929,0.4136,0.98823,0.98851,0.48774,0.5215,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68461,SRR17745589,SRX13908023,SRS11764624,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Propy 1uM Lymph TCGACGTC CTTAATAG,GSM5835366,,tissue:TCGACGTC CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Propy 1uM Lymph TCGACGTC CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,TCGACGTC CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835366,GSM5835366: Naive Propy 1uM Lymph TCGACGTC CTTAATAG; Danio rerio; RNA Seq,GSM5835366 r1,GSM5835366,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,TCGACGTC_CTTAATAG.1.fastq.gz TCGACGTC_CTTAATAG.2.fastq.gz,fastq fastq,6092160.0,80160.0,GSM5835366 r1,0:38 1:38,A:662380;C:2047526;G:2527860;T:852969;N:1425,38,38,,,662380,2047526,2527860,852969,1425,SRX13908023,SRS11764624,,,Brigham and Women's Hospital,2,0.27318,0.29675,0.25438,0.27694,0.99028,0.98993,0.45922,0.48916,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68462,SRR17745590,SRX13908022,SRS11764622,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Propy 1uM Lymph TGCAGCTA CTTAATAG,GSM5835365,,tissue:TGCAGCTA CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Propy 1uM Lymph TGCAGCTA CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,TGCAGCTA CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835365,GSM5835365: Naive Propy 1uM Lymph TGCAGCTA CTTAATAG; Danio rerio; RNA Seq,GSM5835365 r1,GSM5835365,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,TGCAGCTA_CTTAATAG.1.fastq.gz TGCAGCTA_CTTAATAG.2.fastq.gz,fastq fastq,8257096.0,108646.0,GSM5835365 r1,0:38 1:38,A:1066272;C:2690396;G:3209739;T:1288965;N:1724,38,38,,,1066272,2690396,3209739,1288965,1724,SRX13908022,SRS11764622,,,Brigham and Women's Hospital,2,0.4422,0.48038,0.42019,0.45702,0.98175,0.98169,0.49729,0.54051,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68463,SRR17745591,SRX13908021,SRS11764621,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Propy 1uM Lymph CGATCAGT CTTAATAG,GSM5835364,,tissue:CGATCAGT CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Propy 1uM Lymph CGATCAGT CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,CGATCAGT CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835364,GSM5835364: Naive Propy 1uM Lymph CGATCAGT CTTAATAG; Danio rerio; RNA Seq,GSM5835364 r1,GSM5835364,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,CGATCAGT_CTTAATAG.1.fastq.gz CGATCAGT_CTTAATAG.2.fastq.gz,fastq fastq,7903240.0,103990.0,GSM5835364 r1,0:38 1:38,A:1206491;C:2450132;G:2883972;T:1360677;N:1968,38,38,,,1206491,2450132,2883972,1360677,1968,SRX13908021,SRS11764621,,,Brigham and Women's Hospital,2,0.66494,0.70291,0.641,0.67728,0.97514,0.97587,0.53022,0.53238,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68464,SRR17745592,SRX13908020,SRS11764620,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Propy 1uM Lymph CCTAAGAC CTTAATAG,GSM5835363,,tissue:CCTAAGAC CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Propy 1uM Lymph CCTAAGAC CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,CCTAAGAC CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835363,GSM5835363: Naive Propy 1uM Lymph CCTAAGAC CTTAATAG; Danio rerio; RNA Seq,GSM5835363 r1,GSM5835363,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,CCTAAGAC_CTTAATAG.1.fastq.gz CCTAAGAC_CTTAATAG.2.fastq.gz,fastq fastq,10207256.0,134306.0,GSM5835363 r1,0:38 1:38,A:1379390;C:3254146;G:3939560;T:1631799;N:2361,38,38,,,1379390,3254146,3939560,1631799,2361,SRX13908020,SRS11764620,,,Brigham and Women's Hospital,2,0.51069,0.5497,0.48117,0.51891,0.97139,0.9721,0.5145,0.5417,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68465,SRR17745593,SRX13908019,SRS11764619,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Propy 20uM Lymph ACTGAGCG CTTAATAG,GSM5835362,,tissue:ACTGAGCG CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Propy 20uM Lymph ACTGAGCG CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,ACTGAGCG CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835362,GSM5835362: Naive Propy 20uM Lymph ACTGAGCG CTTAATAG; Danio rerio; RNA Seq,GSM5835362 r1,GSM5835362,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,ACTGAGCG_CTTAATAG.1.fastq.gz ACTGAGCG_CTTAATAG.2.fastq.gz,fastq fastq,17437592.0,229442.0,GSM5835362 r1,0:38 1:38,A:3284965;C:5167208;G:5462993;T:3517612;N:4814,38,38,,,3284965,5167208,5462993,3517612,4814,SRX13908019,SRS11764619,,,Brigham and Women's Hospital,2,0.83846,0.85435,0.81656,0.83256,0.95022,0.95213,0.52282,0.50221,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68466,SRR17745594,SRX13908018,SRS11764618,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Propy 20uM Lymph TAGCGCTC CTTAATAG,GSM5835361,,tissue:TAGCGCTC CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Propy 20uM Lymph TAGCGCTC CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,TAGCGCTC CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835361,GSM5835361: Naive Propy 20uM Lymph TAGCGCTC CTTAATAG; Danio rerio; RNA Seq,GSM5835361 r1,GSM5835361,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,TAGCGCTC_CTTAATAG.1.fastq.gz TAGCGCTC_CTTAATAG.2.fastq.gz,fastq fastq,27331120.0,359620.0,GSM5835361 r1,0:38 1:38,A:5099233;C:8072742;G:8617771;T:5534605;N:6769,38,38,,,5099233,8072742,8617771,5534605,6769,SRX13908018,SRS11764618,,,Brigham and Women's Hospital,2,0.78447,0.80834,0.76324,0.78736,0.95199,0.95463,0.52541,0.52334,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68467,SRR17745595,SRX13908017,SRS11764617,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Propy 20uM Lymph ATGCGCAG CTTAATAG,GSM5835360,,tissue:ATGCGCAG CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Propy 20uM Lymph ATGCGCAG CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,ATGCGCAG CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835360,GSM5835360: Naive Propy 20uM Lymph ATGCGCAG CTTAATAG; Danio rerio; RNA Seq,GSM5835360 r1,GSM5835360,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,ATGCGCAG_CTTAATAG.1.fastq.gz ATGCGCAG_CTTAATAG.2.fastq.gz,fastq fastq,7300104.0,96054.0,GSM5835360 r1,0:38 1:38,A:1299284;C:2142705;G:2421373;T:1434665;N:2077,38,38,,,1299284,2142705,2421373,1434665,2077,SRX13908017,SRS11764617,,,Brigham and Women's Hospital,2,0.71631,0.76036,0.68818,0.73112,0.97108,0.97252,0.54776,0.5562,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68468,SRR17745596,SRX13908016,SRS11764616,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Propy 20uM Lymph TACGCTGC CTTAATAG,GSM5835359,,tissue:TACGCTGC CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Propy 20uM Lymph TACGCTGC CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,TACGCTGC CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835359,GSM5835359: Naive Propy 20uM Lymph TACGCTGC CTTAATAG; Danio rerio; RNA Seq,GSM5835359 r1,GSM5835359,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,TACGCTGC_CTTAATAG.1.fastq.gz TACGCTGC_CTTAATAG.2.fastq.gz,fastq fastq,50598824.0,665774.0,GSM5835359 r1,0:38 1:38,A:10026795;C:14117540;G:15701584;T:10739552;N:13353,38,38,,,10026795,14117540,15701584,10739552,13353,SRX13908016,SRS11764616,,,Brigham and Women's Hospital,2,0.76295,0.78356,0.72698,0.74687,0.92784,0.93016,0.5389,0.5429,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68469,SRR17745597,SRX13908015,SRS11764615,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Control 0uM Lymph CGGAGCCT CTTAATAG,GSM5835358,,tissue:CGGAGCCT CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Control 0uM Lymph CGGAGCCT CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,CGGAGCCT CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835358,GSM5835358: Naive Control 0uM Lymph CGGAGCCT CTTAATAG; Danio rerio; RNA Seq,GSM5835358 r1,GSM5835358,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,CGGAGCCT_CTTAATAG.1.fastq.gz CGGAGCCT_CTTAATAG.2.fastq.gz,fastq fastq,12008836.0,158011.0,GSM5835358 r1,0:38 1:38,A:1996134;C:3633783;G:4131965;T:2243758;N:3196,38,38,,,1996134,3633783,4131965,2243758,3196,SRX13908015,SRS11764615,,,Brigham and Women's Hospital,2,0.62464,0.65559,0.6019,0.63142,0.96566,0.96575,0.49372,0.50661,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68470,SRR17745598,SRX13908014,SRS11764614,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Control 0uM Lymph GCGTAGTA CTTAATAG,GSM5835357,,tissue:GCGTAGTA CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Control 0uM Lymph GCGTAGTA CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,GCGTAGTA CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835357,GSM5835357: Naive Control 0uM Lymph GCGTAGTA CTTAATAG; Danio rerio; RNA Seq,GSM5835357 r1,GSM5835357,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,GCGTAGTA_CTTAATAG.1.fastq.gz GCGTAGTA_CTTAATAG.2.fastq.gz,fastq fastq,18710440.0,246190.0,GSM5835357 r1,0:38 1:38,A:3732933;C:5220156;G:5738632;T:4013080;N:5639,38,38,,,3732933,5220156,5738632,4013080,5639,SRX13908014,SRS11764614,,,Brigham and Women's Hospital,2,0.7347,0.76068,0.70208,0.72909,0.92868,0.9347,0.49423,0.49496,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68471,SRR17745599,SRX13908013,SRS11764613,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Control 0uM Lymph GGAGCTAC CTTAATAG,GSM5835356,,tissue:GGAGCTAC CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Control 0uM Lymph GGAGCTAC CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,GGAGCTAC CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835356,GSM5835356: Naive Control 0uM Lymph GGAGCTAC CTTAATAG; Danio rerio; RNA Seq,GSM5835356 r1,GSM5835356,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,GGAGCTAC_CTTAATAG.1.fastq.gz GGAGCTAC_CTTAATAG.2.fastq.gz,fastq fastq,3102244.0,40819.0,GSM5835356 r1,0:38 1:38,A:496570;C:958082;G:1106726;T:540152;N:714,38,38,,,496570,958082,1106726,540152,714,SRX13908013,SRS11764613,,,Brigham and Women's Hospital,2,0.73692,0.7652,0.71138,0.73975,0.98733,0.98776,0.49216,0.49157,38,38,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68472,SRR17745600,SRX13908012,SRS11764612,SRP356703,PRJNA800448,RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model,GSE194408,Transcriptome Analysis,Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment  4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment.,parent bioproject:PRJNA800443,pubmed:36266581,,Naive Control 0uM Lymph ACTCGCTA CTTAATAG,GSM5835355,,tissue:ACTCGCTA CTTAATAG|strain:AB|Sex:NA|age:NA,Naive Control 0uM Lymph ACTCGCTA CTTAATAG,The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto,ACTCGCTA CTTAATAG,N/A,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,N/A,strain:AB|Sex:NA|age:NA,GSM5835355,GSM5835355: Naive Control 0uM Lymph ACTCGCTA CTTAATAG; Danio rerio; RNA Seq,GSM5835355 r1,GSM5835355,1,N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356703,,,ACTCGCTA_CTTAATAG.1.fastq.gz ACTCGCTA_CTTAATAG.2.fastq.gz,fastq fastq,55052500.0,724375.0,GSM5835355 r1,0:38 1:38,A:13186245;C:13693117;G:14305285;T:13851635;N:16218,38,38,,,13186245,13693117,14305285,13851635,16218,SRX13908012,SRS11764612,,,Brigham and Women's Hospital,2,0.02154,0.02131,0.0166,0.01627,0.99188,0.99194,0.46358,0.47281,38,38,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-25,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
68887,SRR18218065,SRX14364509,SRS12177804,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 5,,strain:CG1|age:133 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:23 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 5,CG1 P2mut STABLE 5,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAURAAPEI-P51E3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAURAAPEI-P51E3_2.fq.gz,fastq fastq,18195264000.0,60650880.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAURAAPEI P51E3 1.fq.gz,0:150 1:150,A:4675448937;C:4456563746;G:4459950645;T:4603273696;N:26976,150,150,,,4675448937,4456563746,4459950645,4603273696,26976,SRX14364509,SRS12177804,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94521,0.94594,0.11243,0.11174,0.79551,0.79496,0.51393,0.51099,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System
68888,SRR18218066,SRX14364508,SRS12177803,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 4,,strain:CG1|age:133 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:23 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 4,CG1 P2mut STABLE 4,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAATRAAPEI-P39D3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAATRAAPEI-P39D3_2.fq.gz,fastq fastq,18145191600.0,60483972.0,FCHT5GHDSXX L1 HKRDZEBmfpEAATRAAPEI P39D3 1.fq.gz,0:150 1:150,A:4669829222;C:4433244502;G:4437119015;T:4604972909;N:25952,150,150,,,4669829222,4433244502,4437119015,4604972909,25952,SRX14364508,SRS12177803,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94405,0.94389,0.11135,0.11157,0.79401,0.79385,0.50436,0.50132,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System
68893,SRR18218072,SRX14364503,SRS12177798,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc 7,,strain:Tu/AB|age:41 days|sex:not collected|tissue:lymphoid|birth date:04 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB,Tu AB mMyc 7,Tu AB mMyc 7,Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAXRAAPEI-P87H3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAXRAAPEI-P87H3_2.fq.gz,fastq fastq,18002105400.0,60007018.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAXRAAPEI P87H3 1.fq.gz,0:150 1:150,A:4483057959;C:4549819065;G:4562924506;T:4406277865;N:26005,150,150,,,4483057959,4549819065,4562924506,4406277865,26005,SRX14364503,SRS12177798,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.9259,0.92681,0.09642,0.09697,0.82479,0.82546,0.50634,0.5148,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System
68894,SRR18218073,SRX14364502,SRS12177797,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc 6,,strain:Tu/AB|age:42 days|sex:not collected|tissue:lymphoid|birth date:03 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB,Tu AB mMyc 6,Tu AB mMyc 6,Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAWRABPEI-P75G3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAWRABPEI-P75G3_2.fq.gz,fastq fastq,18085463400.0,60284878.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAWRABPEI P75G3 1.fq.gz,0:150 1:150,A:4716166539;C:4371919988;G:4399782048;T:4597568953;N:25872,150,150,,,4716166539,4371919988,4399782048,4597568953,25872,SRX14364502,SRS12177797,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.90432,0.90596,0.06444,0.06367,0.80048,0.80095,0.51671,0.51624,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System
68895,SRR18218074,SRX14364501,SRS12177796,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc 5,,strain:Tu/AB|age:42 days|sex:not collected|tissue:lymphoid|birth date:03 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB,Tu AB mMyc 5,Tu AB mMyc 5,Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAVRAAPEI-P63F3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAVRAAPEI-P63F3_2.fq.gz,fastq fastq,18063312600.0,60211042.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAVRAAPEI P63F3 1.fq.gz,0:150 1:150,A:4440821008;C:4618318980;G:4635597240;T:4368548938;N:26434,150,150,,,4440821008,4618318980,4635597240,4368548938,26434,SRX14364501,SRS12177796,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.91708,0.91735,0.0319,0.0316,0.80793,0.80744,0.50004,0.5071,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System
68896,SRR18218075,SRX14364500,SRS12177795,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 3,,strain:CG1|age:121 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:11 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 3,CG1 P2mut STABLE 3,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAASRAAPEI-P27C3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAASRAAPEI-P27C3_2.fq.gz,fastq fastq,18163928100.0,60546427.0,FCHT5GHDSXX L1 HKRDZEBmfpEAASRAAPEI P27C3 1.fq.gz,0:150 1:150,A:4642188606;C:4470457895;G:4476885626;T:4574370149;N:25824,150,150,,,4642188606,4470457895,4476885626,4574370149,25824,SRX14364500,SRS12177795,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94449,0.94468,0.0858,0.0861,0.77114,0.7696,0.52498,0.52464,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System
68897,SRR18218076,SRX14364499,SRS12177794,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc+P2mut 4,,strain:Tu/AB|age:28 days|sex:not collected|tissue:lymphoid|birth date:08 02 2017|death date:08 03 2017|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut2|biological replicate:Tu AB mMyc+P1mut biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB,Tu AB mMyc+P2mut 4,Tu AB mMyc+P2mut 4,Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEABBRAAPEI-P40D4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEABBRAAPEI-P40D4_2.fq.gz,fastq fastq,18117791400.0,60392638.0,FCHT5GHDSXX L1 HKRDZEBmfpEABBRAAPEI P40D4 1.fq.gz,0:150 1:150,A:4565894721;C:4513701269;G:4551999162;T:4486169550;N:26698,150,150,,,4565894721,4513701269,4551999162,4486169550,26698,SRX14364499,SRS12177794,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94,0.93956,0.08699,0.08679,0.81941,0.81832,0.51722,0.51946,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Larval,Larval,Lymphatic System,Cardiovascular System
68898,SRR18218077,SRX14364498,SRS12177793,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc+P1mut 6,,strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB,Tu AB mMyc+P1mut 6,Tu AB mMyc+P1mut 6,Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEABARAAPEI-P28C4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEABARAAPEI-P28C4_2.fq.gz,fastq fastq,18034321800.0,60114406.0,FCHT5GHDSXX L1 HKRDZEBmfpEABARAAPEI P28C4 1.fq.gz,0:150 1:150,A:4518122158;C:4519676234;G:4543758117;T:4452738564;N:26727,150,150,,,4518122158,4519676234,4543758117,4452738564,26727,SRX14364498,SRS12177793,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94431,0.94437,0.10494,0.10462,0.83177,0.83037,0.51143,0.51642,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System
68899,SRR18218078,SRX14364497,SRS12177792,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc+P1mut 5,,strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB,Tu AB mMyc+P1mut 5,Tu AB mMyc+P1mut 5,Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAZRAAPEI-P16B4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAZRAAPEI-P16B4_2.fq.gz,fastq fastq,17750634300.0,59168781.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAZRAAPEI P16B4 1.fq.gz,0:150 1:150,A:4503506819;C:4398697723;G:4432972998;T:4415430837;N:25923,150,150,,,4503506819,4398697723,4432972998,4415430837,25923,SRX14364497,SRS12177792,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94306,0.94321,0.07511,0.0748,0.79837,0.79819,0.51326,0.50902,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System
68900,SRR18218079,SRX14364496,SRS12177791,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc+P1mut 4,,strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB,Tu AB mMyc+P1mut 4,Tu AB mMyc+P1mut 4,Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAYRAAPEI-P4A4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAYRAAPEI-P4A4_2.fq.gz,fastq fastq,18063110700.0,60210369.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAYRAAPEI P4A4 1.fq.gz,0:150 1:150,A:4583950532;C:4496933352;G:4489104841;T:4493095718;N:26257,150,150,,,4583950532,4496933352,4489104841,4493095718,26257,SRX14364496,SRS12177791,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.95231,0.9534,0.12525,0.12554,0.84404,0.84323,0.52132,0.53078,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System
68911,SRR18218090,SRX14364485,SRS12177780,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 2,,strain:CG1|age:121 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:11 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 2,CG1 P2mut STABLE 2,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAARRAAPEI-P15B3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAARRAAPEI-P15B3_2.fq.gz,fastq fastq,18103313700.0,60344379.0,FCHT5GHDSXX L1 HKRDZEBmfpEAARRAAPEI P15B3 1.fq.gz,0:150 1:150,A:4586370941;C:4481640272;G:4519408464;T:4515867439;N:26584,150,150,,,4586370941,4481640272,4519408464,4515867439,26584,SRX14364485,SRS12177780,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94376,0.94365,0.11084,0.10978,0.79847,0.79788,0.52621,0.52367,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System
68912,SRR18218091,SRX14364484,SRS12177779,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce  T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations  10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha  encoded by IL7R  which occur in different molecular subtypes of this disease. However  it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also  which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here  we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally  we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways  harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover  limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 1,,strain:CG1|age:121 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:11 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 1,CG1 P2mut STABLE 1,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT  fragmented and converted to cDNA  size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAQRAAPEI-P3A3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAQRAAPEI-P3A3_2.fq.gz,fastq fastq,18068692800.0,60228976.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAQRAAPEI P3A3 1.fq.gz,0:150 1:150,A:4592071905;C:4477973011;G:4471601663;T:4527019823;N:26398,150,150,,,4592071905,4477973011,4471601663,4527019823,26398,SRX14364484,SRS12177779,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94814,0.94931,0.09511,0.09463,0.79756,0.79762,0.51602,0.51609,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System