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52 rows where experiment.library_selection = "cDNA" and tissue_curation = "Lymphatic System"

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tissue_curation 1

  • Lymphatic System · 52 ✖

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experiment.library_strategy 1

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experiment.library_selection 1

  • cDNA · 52 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
61414 61414 SRR12712225 SRX9191123 SRS7427095 SRP285378 PRJNA665656 The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish] GSE158566 Transcriptome Analysis The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos parent bioproject:PRJNA748172     ddx21 sibling 02 GSM4802983   tissue:ddx21 sibling|genotype/variation:ddx21 sibling|abbreviatedname:Sib 02|cell type:venous and lymphatic ECs VECs LECs ddx21 sibling 02 Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample ddx21 sibling   At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:ddx21 sibling|abbreviatedname:Sib 02|cell type:venous and lymphatic ECs VECs LECs GSM4802983 GSM4802983: ddx21 sibling 02; Danio rerio; RNA Seq GSM4802983   1 At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4802983 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP285378     4-DDX_sibling2_S5_R1_001.fastq fastq 4132086148.0 54841271.0 GSM4802983 r1 0:75.35 1:0 A:1143149123;C:915565985;G:945819940;T:1127493713;N:57387 75 0     1143149123 915565985 945819940 1127493713 57387 SRX9191123 SRS7427095 SRA1131557 GEO Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre 1 0.93153   0.15182   0.73127   0.47996   75   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2020-09-25 Larval Larval Lymphatic System Cardiovascular System
61415 61415 SRR12712224 SRX9191122 SRS7427094 SRP285378 PRJNA665656 The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish] GSE158566 Transcriptome Analysis The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos parent bioproject:PRJNA748172     ddx21 mutant 02 GSM4802982   tissue:ddx21 mutant|genotype/variation:ddx21 mutant|abbreviatedname:Mut 02|cell type:venous and lymphatic ECs VECs LECs ddx21 mutant 02 Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample ddx21 mutant   At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:ddx21 mutant|abbreviatedname:Mut 02|cell type:venous and lymphatic ECs VECs LECs GSM4802982 GSM4802982: ddx21 mutant 02; Danio rerio; RNA Seq GSM4802982   1 At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4802982 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP285378     3-DDX1_mutant2_S6_R1_001.fastq fastq 4489565415.0 59577710.0 GSM4802982 r1 0:75.36 1:0 A:1250571429;C:986785347;G:1019382421;T:1232761308;N:64910 75 0     1250571429 986785347 1019382421 1232761308 64910 SRX9191122 SRS7427094 SRA1131557 GEO Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre 1 0.93491   0.11271   0.7399   0.48877   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2020-09-25 Larval Larval Lymphatic System Cardiovascular System
61416 61416 SRR12712223 SRX9191121 SRS7427093 SRP285378 PRJNA665656 The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish] GSE158566 Transcriptome Analysis The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos parent bioproject:PRJNA748172     ddx21 sibling 01 GSM4802981   tissue:ddx21 sibling|genotype/variation:ddx21 sibling|abbreviatedname:Sib 01|cell type:venous and lymphatic ECs VECs LECs ddx21 sibling 01 Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample ddx21 sibling   At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:ddx21 sibling|abbreviatedname:Sib 01|cell type:venous and lymphatic ECs VECs LECs GSM4802981 GSM4802981: ddx21 sibling 01; Danio rerio; RNA Seq GSM4802981   1 At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4802981 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP285378     2-DDX_sibling1_S7_R1_001.fastq fastq 3962887115.0 52588574.0 GSM4802981 r1 0:75.36 1:0 A:1113967875;C:858353708;G:888913973;T:1101593170;N:58389 75 0     1113967875 858353708 888913973 1101593170 58389 SRX9191121 SRS7427093 SRA1131557 GEO Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre 1 0.92594   0.17769   0.72143   0.49105   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2020-09-25 Larval Larval Lymphatic System Cardiovascular System
61417 61417 SRR12712222 SRX9191120 SRS7427092 SRP285378 PRJNA665656 The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish] GSE158566 Transcriptome Analysis The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos parent bioproject:PRJNA748172     ddx21 mutant 01 GSM4802980   tissue:ddx21 mutant|genotype/variation:ddx21 mutant|abbreviatedname:Mut 01|cell type:venous and lymphatic ECs VECs LECs ddx21 mutant 01 Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample ddx21 mutant   At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:ddx21 mutant|abbreviatedname:Mut 01|cell type:venous and lymphatic ECs VECs LECs GSM4802980 GSM4802980: ddx21 mutant 01; Danio rerio; RNA Seq GSM4802980   1 At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4802980 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP285378     1-DDX1_mutant1_S8_R1_001.fastq fastq 4172788466.0 55358419.0 GSM4802980 r1 0:75.38 1:0 A:1157297483;C:922321451;G:952921150;T:1140193401;N:54981 75 0     1157297483 922321451 952921150 1140193401 54981 SRX9191120 SRS7427092 SRA1131557 GEO Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre 1 0.93753   0.11708   0.75022   0.4679   74   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2020-09-25 Larval Larval Lymphatic System Cardiovascular System
61418 61418 SRR12712229 SRX9191119 SRS7427091 SRP285378 PRJNA665656 The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish] GSE158566 Transcriptome Analysis The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos parent bioproject:PRJNA748172     ddx21 sibling 04 GSM4802987   tissue:ddx21 sibling|genotype/variation:ddx21 sibling|abbreviatedname:Sib 04|cell type:venous and lymphatic ECs VECs LECs ddx21 sibling 04 Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample ddx21 sibling   At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:ddx21 sibling|abbreviatedname:Sib 04|cell type:venous and lymphatic ECs VECs LECs GSM4802987 GSM4802987: ddx21 sibling 04; Danio rerio; RNA Seq GSM4802987   1 At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4802987 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP285378     8-DDX_sibling4_S1_R1_001.fastq fastq 4915017825.0 65191268.0 GSM4802987 r1 0:75.39 1:0 A:1371356175;C:1074769694;G:1111138012;T:1357694052;N:59892 75 0     1371356175 1074769694 1111138012 1357694052 59892 SRX9191119 SRS7427091 SRA1131557 GEO Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre 1 0.93029   0.13059   0.76288   0.49579   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2020-09-25 Larval Larval Lymphatic System Cardiovascular System
61419 61419 SRR12712228 SRX9191118 SRS7427090 SRP285378 PRJNA665656 The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish] GSE158566 Transcriptome Analysis The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos parent bioproject:PRJNA748172     ddx21 mutant 04 GSM4802986   tissue:ddx21 mutant|genotype/variation:ddx21 mutant|abbreviatedname:Mut 04|cell type:venous and lymphatic ECs VECs LECs ddx21 mutant 04 Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample ddx21 mutant   At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:ddx21 mutant|abbreviatedname:Mut 04|cell type:venous and lymphatic ECs VECs LECs GSM4802986 GSM4802986: ddx21 mutant 04; Danio rerio; RNA Seq GSM4802986   1 At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4802986 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP285378     7-DDX1_mutant4_S2_R1_001.fastq fastq 4934798895.0 65454382.0 GSM4802986 r1 0:75.39 1:0 A:1386796418;C:1074595432;G:1108772428;T:1364575960;N:58657 75 0     1386796418 1074595432 1108772428 1364575960 58657 SRX9191118 SRS7427090 SRA1131557 GEO Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre 1 0.93352   0.1274   0.75276   0.49744   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2020-09-25 Larval Larval Lymphatic System Cardiovascular System
61420 61420 SRR12712227 SRX9191117 SRS7427089 SRP285378 PRJNA665656 The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish] GSE158566 Transcriptome Analysis The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos parent bioproject:PRJNA748172     ddx21 sibling 03 GSM4802985   tissue:ddx21 sibling|genotype/variation:ddx21 sibling|abbreviatedname:Sib 03|cell type:venous and lymphatic ECs VECs LECs ddx21 sibling 03 Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample ddx21 sibling   At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:ddx21 sibling|abbreviatedname:Sib 03|cell type:venous and lymphatic ECs VECs LECs GSM4802985 GSM4802985: ddx21 sibling 03; Danio rerio; RNA Seq GSM4802985   1 At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4802985 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP285378     6-DDX_sibling3_S3_R1_001.fastq fastq 4686029757.0 62155887.0 GSM4802985 r1 0:75.39 1:0 A:1310041056;C:1025050637;G:1061770975;T:1289110659;N:56430 75 0     1310041056 1025050637 1061770975 1289110659 56430 SRX9191117 SRS7427089 SRA1131557 GEO Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre 1 0.93421   0.13013   0.74468   0.50075   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2020-09-25 Larval Larval Lymphatic System Cardiovascular System
61421 61421 SRR12712226 SRX9191116 SRS7427088 SRP285378 PRJNA665656 The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish] GSE158566 Transcriptome Analysis The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos parent bioproject:PRJNA748172     ddx21 mutant 03 GSM4802984   tissue:ddx21 mutant|genotype/variation:ddx21 mutant|abbreviatedname:Mut 03|cell type:venous and lymphatic ECs VECs LECs ddx21 mutant 03 Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample ddx21 mutant   At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:ddx21 mutant|abbreviatedname:Mut 03|cell type:venous and lymphatic ECs VECs LECs GSM4802984 GSM4802984: ddx21 mutant 03; Danio rerio; RNA Seq GSM4802984   1 At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4802984 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP285378     5-DDX1_mutant3_S4_R1_001.fastq fastq 4774244717.0 63335788.0 GSM4802984 r1 0:75.38 1:0 A:1333800977;C:1045188899;G:1081436862;T:1313758360;N:59619 75 0     1333800977 1045188899 1081436862 1313758360 59619 SRX9191116 SRS7427088 SRA1131557 GEO Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre 1 0.93177   0.13392   0.73864   0.49841   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2020-09-25 Larval Larval Lymphatic System Cardiovascular System
68437 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;