{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.platform = \"ILLUMINA\", technology = \"celseq\" and tissue_curation = \"Kidney\"", "rows": [[47861, "SRR6908751", "SRX3856810", "SRS3100403", "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.", null, "pubmed:31585086", null, "WKM9 unenriched", "GSM3070148", null, "tissue:WKM9 unenriched|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM9 unenriched", "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. 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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.", null, "pubmed:31585086", null, "WKM9 unenriched", "GSM3070148", null, "tissue:WKM9 unenriched|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM9 unenriched", "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. 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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.", null, "pubmed:31585086", null, "WKM9 monocytes", "GSM3070147", null, "tissue:WKM9 monocytes|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM9 monocytes", "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", "WKM9 monocytes", null, "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", null, "FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070147", "GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq", "GSM3070147", null, "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:GSM3070147", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM9_monocytes_L001_R1_001.fastq.gz WKM9_monocytes_L001_R2_001.fastq.gz", "fastq fastq", 1661471905.0, 11011987.0, "GSM3070147 r1", "0:75.40 1:75.48", "A:483808436;C:239092096;G:277634836;T:660929005;N:7532", 75, 75, null, null, 483808436, 239092096, 277634836, 660929005, 7532, "SRX3856809", "SRS3100401", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.36065, 0.81129, 0.26031, 0.39596, 0.96376, 0.87584, 0.46482, 0.51218, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47866, "SRR6908748", "SRX3856809", "SRS3100401", "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.", null, "pubmed:31585086", null, "WKM9 monocytes", "GSM3070147", null, "tissue:WKM9 monocytes|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM9 monocytes", "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", "WKM9 monocytes", null, "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", null, "FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070147", "GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq", "GSM3070147", null, "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:GSM3070147", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM9_monocytes_L002_R1_001.fastq.gz WKM9_monocytes_L002_R2_001.fastq.gz", "fastq fastq", 1643858405.0, 10895074.0, "GSM3070147 r2", "0:75.40 1:75.48", "A:474610672;C:235181134;G:281183851;T:652878617;N:4131", 75, 75, null, null, 474610672, 235181134, 281183851, 652878617, 4131, "SRX3856809", "SRS3100401", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.35844, 0.80892, 0.26121, 0.38966, 0.96631, 0.88008, 0.45688, 0.49263, 74, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47867, "SRR6908749", "SRX3856809", "SRS3100401", "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.", null, "pubmed:31585086", null, "WKM9 monocytes", "GSM3070147", null, "tissue:WKM9 monocytes|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM9 monocytes", "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", "WKM9 monocytes", null, "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", null, "FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070147", "GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq", "GSM3070147", null, "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:GSM3070147", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM9_monocytes_L003_R1_001.fastq.gz WKM9_monocytes_L003_R2_001.fastq.gz", "fastq fastq", 1503593728.0, 9965072.0, "GSM3070147 r3", "0:75.41 1:75.48", "A:435191543;C:215315484;G:255248972;T:597807800;N:29929", 75, 75, null, null, 435191543, 215315484, 255248972, 597807800, 29929, "SRX3856809", "SRS3100401", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.3504, 0.80674, 0.25495, 0.3888, 0.96974, 0.88402, 0.4596, 0.50684, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47868, "SRR6908750", "SRX3856809", "SRS3100401", "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.", null, "pubmed:31585086", null, "WKM9 monocytes", "GSM3070147", null, "tissue:WKM9 monocytes|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM9 monocytes", "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", "WKM9 monocytes", null, "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", null, "FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070147", "GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq", "GSM3070147", null, "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:GSM3070147", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM9_monocytes_L004_R1_001.fastq.gz WKM9_monocytes_L004_R2_001.fastq.gz", "fastq fastq", 1474164037.0, 9770113.0, "GSM3070147 r4", "0:75.41 1:75.48", "A:425654229;C:209255453;G:253849148;T:585380972;N:24235", 75, 75, null, null, 425654229, 209255453, 253849148, 585380972, 24235, "SRX3856809", "SRS3100401", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.36215, 0.81922, 0.26584, 0.39594, 0.97096, 0.89171, 0.46223, 0.51731, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47873, "SRR6908739", "SRX3856807", "SRS3100399", "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.", null, "pubmed:31585086", null, "WKM8 unenriched", "GSM3070145", null, "tissue:WKM8 unenriched|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM8 unenriched", "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", "WKM8 unenriched", null, "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", null, "FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070145", "GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq", "GSM3070145", null, "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:GSM3070145", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM8_unenriched_L001_R1_001.fastq.gz WKM8_unenriched_L001_R2_001.fastq.gz", "fastq fastq", 1667087336.0, 11048469.0, "GSM3070145 r1", "0:75.40 1:75.49", "A:475560256;C:240713376;G:276116899;T:674689422;N:7383", 75, 75, null, null, 475560256, 240713376, 276116899, 674689422, 7383, "SRX3856807", "SRS3100399", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.39157, 0.8295, 0.26694, 0.3429, 0.95806, 0.85117, 0.47471, 0.5079, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47874, "SRR6908740", "SRX3856807", "SRS3100399", "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.", null, "pubmed:31585086", null, "WKM8 unenriched", "GSM3070145", null, "tissue:WKM8 unenriched|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM8 unenriched", "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", "WKM8 unenriched", null, "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", null, "FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070145", "GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq", "GSM3070145", null, "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:GSM3070145", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM8_unenriched_L002_R1_001.fastq.gz WKM8_unenriched_L002_R2_001.fastq.gz", "fastq fastq", 1643985440.0, 10895186.0, "GSM3070145 r2", "0:75.40 1:75.49", "A:465022994;C:236298663;G:278363355;T:664296206;N:4222", 75, 75, null, null, 465022994, 236298663, 278363355, 664296206, 4222, "SRX3856807", "SRS3100399", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.38307, 0.82794, 0.26079, 0.33908, 0.95966, 0.85573, 0.47886, 0.53225, 76, 74, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47875, "SRR6908741", "SRX3856807", "SRS3100399", "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.", null, "pubmed:31585086", null, "WKM8 unenriched", "GSM3070145", null, "tissue:WKM8 unenriched|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM8 unenriched", "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", "WKM8 unenriched", null, "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", null, "FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070145", "GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq", "GSM3070145", null, "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:GSM3070145", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM8_unenriched_L003_R1_001.fastq.gz WKM8_unenriched_L003_R2_001.fastq.gz", "fastq fastq", 1497995831.0, 9927192.0, "GSM3070145 r3", "0:75.41 1:75.48", "A:423994108;C:216014805;G:251009522;T:606949772;N:27624", 75, 75, null, null, 423994108, 216014805, 251009522, 606949772, 27624, "SRX3856807", "SRS3100399", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.37662, 0.82297, 0.26009, 0.33859, 0.96382, 0.8616, 0.4713, 0.53853, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47876, "SRR6908742", "SRX3856807", "SRS3100399", "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.", null, "pubmed:31585086", null, "WKM8 unenriched", "GSM3070145", null, "tissue:WKM8 unenriched|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM8 unenriched", "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", "WKM8 unenriched", null, "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", null, "FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070145", "GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq", "GSM3070145", null, "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:GSM3070145", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM8_unenriched_L004_R1_001.fastq.gz WKM8_unenriched_L004_R2_001.fastq.gz", "fastq fastq", 1462948321.0, 9695189.0, "GSM3070145 r4", "0:75.41 1:75.48", "A:413526172;C:209432303;G:247960945;T:592005236;N:23665", 75, 75, null, null, 413526172, 209432303, 247960945, 592005236, 23665, "SRX3856807", "SRS3100399", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.39195, 0.83802, 0.26623, 0.34329, 0.96301, 0.86659, 0.47028, 0.53168, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47877, "SRR6908735", "SRX3856806", "SRS3100398", "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.", null, "pubmed:31585086", null, "WKM8 monocytes", "GSM3070144", null, "tissue:WKM8 monocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM8 monocytes", "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", "WKM8 monocytes", null, "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", null, "FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070144", "GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq", "GSM3070144", null, "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:GSM3070144", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM8_monocytes_L001_R1_001.fastq.gz WKM8_monocytes_L001_R2_001.fastq.gz", "fastq fastq", 930630033.0, 6164203.0, "GSM3070144 r1", "0:75.50 1:75.47", "A:258982746;C:129522885;G:148763386;T:393303395;N:57621", 75, 75, null, null, 258982746, 129522885, 148763386, 393303395, 57621, "SRX3856806", "SRS3100398", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.32023, 0.84288, 0.2067, 0.29948, 0.98628, 0.9247, 0.4816, 0.56903, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47878, "SRR6908736", "SRX3856806", "SRS3100398", "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.", null, "pubmed:31585086", null, "WKM8 monocytes", "GSM3070144", null, "tissue:WKM8 monocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM8 monocytes", "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", "WKM8 monocytes", null, "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", null, "FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070144", "GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq", "GSM3070144", null, "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:GSM3070144", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM8_monocytes_L002_R1_001.fastq.gz WKM8_monocytes_L002_R2_001.fastq.gz", "fastq fastq", 840139689.0, 5565664.0, "GSM3070144 r2", "0:75.50 1:75.45", "A:236179715;C:116541374;G:133572472;T:353806731;N:39397", 75, 75, null, null, 236179715, 116541374, 133572472, 353806731, 39397, "SRX3856806", "SRS3100398", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.28608, 0.81641, 0.18643, 0.30235, 0.99159, 0.94799, 0.46036, 0.51728, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47879, "SRR6908737", "SRX3856806", "SRS3100398", "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.", null, "pubmed:31585086", null, "WKM8 monocytes", "GSM3070144", null, "tissue:WKM8 monocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM8 monocytes", "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", "WKM8 monocytes", null, "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", null, "FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070144", "GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq", "GSM3070144", null, "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:GSM3070144", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM8_monocytes_L003_R2_001.fastq.gz WKM8_monocytes_L003_R1_001.fastq.gz", "fastq fastq", 829094700.0, 5491203.0, "GSM3070144 r3", "0:75.52 1:75.47", "A:229473245;C:115123563;G:132541877;T:351944469;N:11546", 75, 75, null, null, 229473245, 115123563, 132541877, 351944469, 11546, "SRX3856806", "SRS3100398", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.27624, 0.83541, 0.18571, 0.30162, 0.99358, 0.93693, 0.46624, 0.58337, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47880, "SRR6908738", "SRX3856806", "SRS3100398", "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.", null, "pubmed:31585086", null, "WKM8 monocytes", "GSM3070144", null, "tissue:WKM8 monocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM8 monocytes", "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", "WKM8 monocytes", null, "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", null, "FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070144", "GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq", "GSM3070144", null, "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:GSM3070144", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM8_monocytes_L004_R1_001.fastq.gz WKM8_monocytes_L004_R2_001.fastq.gz", "fastq fastq", 717316840.0, 4751642.0, "GSM3070144 r4", "0:75.51 1:75.45", "A:201002776;C:99055550;G:115888860;T:301362855;N:6799", 75, 75, null, null, 201002776, 99055550, 115888860, 301362855, 6799, "SRX3856806", "SRS3100398", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.24919, 0.82101, 0.16961, 0.29185, 0.99543, 0.94882, 0.43582, 0.58134, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47885, "SRR6908727", "SRX3856804", "SRS3100396", "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.", null, "pubmed:31585086", null, "WKM7 unenriched", "GSM3070142", null, "tissue:WKM7 unenriched|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM7 unenriched", "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", "WKM7 unenriched", null, "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", null, "FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070142", "GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq", "GSM3070142", null, "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:GSM3070142", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM7_unenriched_L001_R1_001.fastq.gz WKM7_unenriched_L001_R2_001.fastq.gz", "fastq fastq", 1470115941.0, 9738991.0, "GSM3070142 r1", "0:75.44 1:75.51", "A:398948568;C:202294647;G:231760451;T:636827163;N:285112", 75, 75, null, null, 398948568, 202294647, 231760451, 636827163, 285112, "SRX3856804", "SRS3100396", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.40309, 0.87046, 0.32221, 0.26166, 0.99233, 0.84327, 0.29642, 0.52123, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47886, "SRR6908728", "SRX3856804", "SRS3100396", "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.", null, "pubmed:31585086", null, "WKM7 unenriched", "GSM3070142", null, "tissue:WKM7 unenriched|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM7 unenriched", "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", "WKM7 unenriched", null, "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", null, "FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070142", "GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq", "GSM3070142", null, "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:GSM3070142", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM7_unenriched_L002_R1_001.fastq.gz WKM7_unenriched_L002_R2_001.fastq.gz", "fastq fastq", 1461695240.0, 9683144.0, "GSM3070142 r2", "0:75.44 1:75.51", "A:394008699;C:201030493;G:233919014;T:632480364;N:256670", 75, 75, null, null, 394008699, 201030493, 233919014, 632480364, 256670, "SRX3856804", "SRS3100396", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.38758, 0.86795, 0.30719, 0.26558, 0.99255, 0.84607, 0.30994, 0.51718, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47887, "SRR6908729", "SRX3856804", "SRS3100396", "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.", null, "pubmed:31585086", null, "WKM7 unenriched", "GSM3070142", null, "tissue:WKM7 unenriched|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM7 unenriched", "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", "WKM7 unenriched", null, "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", null, "FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070142", "GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq", "GSM3070142", null, "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:GSM3070142", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM7_unenriched_L003_R1_001.fastq.gz WKM7_unenriched_L003_R2_001.fastq.gz", "fastq fastq", 1418045610.0, 9393861.0, "GSM3070142 r3", "0:75.45 1:75.51", "A:383399208;C:195487055;G:222663120;T:616484616;N:11611", 75, 75, null, null, 383399208, 195487055, 222663120, 616484616, 11611, "SRX3856804", "SRS3100396", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.41019, 0.87176, 0.32985, 0.2642, 0.99338, 0.8452, 0.2589, 0.52225, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47888, "SRR6908730", "SRX3856804", "SRS3100396", "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.", null, "pubmed:31585086", null, "WKM7 unenriched", "GSM3070142", null, "tissue:WKM7 unenriched|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM7 unenriched", "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", "WKM7 unenriched", null, "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", null, "FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070142", "GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq", "GSM3070142", null, "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:GSM3070142", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM7_unenriched_L004_R1_001.fastq.gz WKM7_unenriched_L004_R2_001.fastq.gz", "fastq fastq", 1401330195.0, 9283131.0, "GSM3070142 r4", "0:75.44 1:75.51", "A:376049927;C:192808560;G:224900456;T:607563117;N:8135", 75, 75, null, null, 376049927, 192808560, 224900456, 607563117, 8135, "SRX3856804", "SRS3100396", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.40071, 0.86588, 0.31811, 0.26185, 0.99263, 0.84569, 0.27227, 0.5224, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47889, "SRR6908723", "SRX3856803", "SRS3100395", "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.", null, "pubmed:31585086", null, "WKM7 monocytes", "GSM3070141", null, "tissue:WKM7 monocytes|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM7 monocytes", "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", "WKM7 monocytes", null, "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", null, "FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070141", "GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq", "GSM3070141", null, "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:GSM3070141", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM7_monocytes_L001_R1_001.fastq.gz WKM7_monocytes_L001_R2_001.fastq.gz", "fastq fastq", 1791125985.0, 11864169.0, "GSM3070141 r1", "0:75.46 1:75.51", "A:485867889;C:238293947;G:271424293;T:795194496;N:345360", 75, 75, null, null, 485867889, 238293947, 271424293, 795194496, 345360, "SRX3856803", "SRS3100395", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.42246, 0.87038, 0.34993, 0.25475, 0.99302, 0.86906, 0.3, 0.50725, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47890, "SRR6908724", "SRX3856803", "SRS3100395", "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.", null, "pubmed:31585086", null, "WKM7 monocytes", "GSM3070141", null, "tissue:WKM7 monocytes|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM7 monocytes", "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", "WKM7 monocytes", null, "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", null, "FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070141", "GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq", "GSM3070141", null, "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:GSM3070141", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM7_monocytes_L002_R1_001.fastq.gz WKM7_monocytes_L002_R2_001.fastq.gz", "fastq fastq", 1792721494.0, 11874637.0, "GSM3070141 r2", "0:75.46 1:75.51", "A:482977185;C:238180503;G:276068534;T:795172908;N:322364", 75, 75, null, null, 482977185, 238180503, 276068534, 795172908, 322364, "SRX3856803", "SRS3100395", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.42187, 0.86585, 0.347, 0.25727, 0.99261, 0.86983, 0.32168, 0.51044, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47891, "SRR6908725", "SRX3856803", "SRS3100395", "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.", null, "pubmed:31585086", null, "WKM7 monocytes", "GSM3070141", null, "tissue:WKM7 monocytes|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM7 monocytes", "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", "WKM7 monocytes", null, "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", null, "FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070141", "GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq", "GSM3070141", null, "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:GSM3070141", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM7_monocytes_L003_R1_001.fastq.gz WKM7_monocytes_L003_R2_001.fastq.gz", "fastq fastq", 1726273948.0, 11434355.0, "GSM3070141 r3", "0:75.46 1:75.51", "A:466721054;C:229970045;G:260445487;T:769123115;N:14247", 75, 75, null, null, 466721054, 229970045, 260445487, 769123115, 14247, "SRX3856803", "SRS3100395", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.43817, 0.86963, 0.36713, 0.25464, 0.99409, 0.87136, 0.28011, 0.50765, 75, 73, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47892, "SRR6908726", "SRX3856803", "SRS3100395", "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.", null, "pubmed:31585086", null, "WKM7 monocytes", "GSM3070141", null, "tissue:WKM7 monocytes|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes", "WKM7 monocytes", "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", "WKM7 monocytes", null, "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", null, "FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes", "GSM3070141", "GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq", "GSM3070141", null, "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:GSM3070141", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM7_monocytes_L004_R1_001.fastq.gz WKM7_monocytes_L004_R2_001.fastq.gz", "fastq fastq", 1706923699.0, 11306267.0, "GSM3070141 r4", "0:75.46 1:75.51", "A:458067525;C:226793433;G:263424046;T:758628361;N:10334", 75, 75, null, null, 458067525, 226793433, 263424046, 758628361, 10334, "SRX3856803", "SRS3100395", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.42414, 0.86508, 0.34964, 0.25009, 0.99375, 0.87198, 0.28225, 0.51467, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47893, "SRR6908717", "SRX3856802", "SRS3100394", "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.", null, "pubmed:31585086", null, "WKM6 unenriched", "GSM3070140", null, "tissue:WKM6 unenriched|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM6 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070140", "GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq", "GSM3070140", null, "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:GSM3070140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM6_unenriched_L001_R1_001.fastq.gz WKM6_unenriched_L001_R2_001.fastq.gz", "fastq fastq", 1091182818.0, 7228537.0, "GSM3070140 r1", "0:75.49 1:75.46", "A:305460604;C:155608830;G:177642198;T:452400520;N:70666", 75, 75, null, null, 305460604, 155608830, 177642198, 452400520, 70666, "SRX3856802", "SRS3100394", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.32983, 0.81725, 0.21464, 0.30328, 0.98524, 0.91348, 0.47654, 0.51388, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47894, "SRR6908718", "SRX3856802", "SRS3100394", "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.", null, "pubmed:31585086", null, "WKM6 unenriched", "GSM3070140", null, "tissue:WKM6 unenriched|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM6 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070140", "GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq", "GSM3070140", null, "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:GSM3070140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM6_unenriched_L002_R1_001.fastq.gz WKM6_unenriched_L002_R2_001.fastq.gz", "fastq fastq", 992904107.0, 6578507.0, "GSM3070140 r2", "0:75.49 1:75.44", "A:280993567;C:141013446;G:160470422;T:410379926;N:46746", 75, 75, null, null, 280993567, 141013446, 160470422, 410379926, 46746, "SRX3856802", "SRS3100394", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.3103, 0.79506, 0.20764, 0.30662, 0.99076, 0.94178, 0.49304, 0.53389, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47895, "SRR6908720", "SRX3856802", "SRS3100394", "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.", null, "pubmed:31585086", null, "WKM6 unenriched", "GSM3070140", null, "tissue:WKM6 unenriched|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM6 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070140", "GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq", "GSM3070140", null, "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:GSM3070140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM6_unenriched_L003_R1_001.fastq.gz WKM6_unenriched_L003_R2_001.fastq.gz", "fastq fastq", 967648040.0, 6409722.0, "GSM3070140 r3", "0:75.51 1:75.46", "A:269841606;C:137530059;G:157502274;T:402760480;N:13621", 75, 75, null, null, 269841606, 137530059, 157502274, 402760480, 13621, "SRX3856802", "SRS3100394", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.304, 0.80424, 0.20488, 0.29857, 0.99383, 0.92894, 0.44008, 0.5232, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47896, "SRR6908722", "SRX3856802", "SRS3100394", "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.", null, "pubmed:31585086", null, "WKM6 unenriched", "GSM3070140", null, "tissue:WKM6 unenriched|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM6 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070140", "GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq", "GSM3070140", null, "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:GSM3070140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM6_unenriched_L004_R1_001.fastq.gz WKM6_unenriched_L004_R2_001.fastq.gz", "fastq fastq", 843966623.0, 5591352.0, "GSM3070140 r4", "0:75.50 1:75.44", "A:238568640;C:119216971;G:138770810;T:347402234;N:7968", 75, 75, null, null, 238568640, 119216971, 138770810, 347402234, 7968, "SRX3856802", "SRS3100394", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.28014, 0.78908, 0.18667, 0.29821, 0.99496, 0.94424, 0.46594, 0.52932, 75, 72, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47901, "SRR6908709", "SRX3856800", "SRS3100392", "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.", null, "pubmed:31585086", null, "WKM5 unenriched", "GSM3070138", null, "tissue:WKM5 unenriched|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM5 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070138", "GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq", "GSM3070138", null, "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:GSM3070138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM5_unenriched_L001_R1_001.fastq.gz WKM5_unenriched_L001_R2_001.fastq.gz", "fastq fastq", 1616915014.0, 10719306.0, "GSM3070138 r1", "0:75.41 1:75.43", "A:470483106;C:225755405;G:263766190;T:656561040;N:349273", 75, 75, null, null, 470483106, 225755405, 263766190, 656561040, 349273, "SRX3856800", "SRS3100392", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.10729, 0.72403, 0.07307, 0.20274, 0.99017, 0.84524, 0.5068, 0.51693, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47902, "SRR6908710", "SRX3856800", "SRS3100392", "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.", null, "pubmed:31585086", null, "WKM5 unenriched", "GSM3070138", null, "tissue:WKM5 unenriched|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM5 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070138", "GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq", "GSM3070138", null, "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:GSM3070138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM5_unenriched_L002_R1_001.fastq.gz WKM5_unenriched_L002_R2_001.fastq.gz", "fastq fastq", 1573355252.0, 10430670.0, "GSM3070138 r2", "0:75.40 1:75.44", "A:458302389;C:217385315;G:261327273;T:636024406;N:315869", 75, 75, null, null, 458302389, 217385315, 261327273, 636024406, 315869, "SRX3856800", "SRS3100392", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.11064, 0.71559, 0.07574, 0.19872, 0.98981, 0.85005, 0.45203, 0.52838, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47903, "SRR6908711", "SRX3856800", "SRS3100392", "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.", null, "pubmed:31585086", null, "WKM5 unenriched", "GSM3070138", null, "tissue:WKM5 unenriched|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM5 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070138", "GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq", "GSM3070138", null, "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:GSM3070138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM5_unenriched_L003_R2_001.fastq.gz WKM5_unenriched_L003_R1_001.fastq.gz", "fastq fastq", 1566951274.0, 10386628.0, "GSM3070138 r3", "0:75.42 1:75.44", "A:451321309;C:220819392;G:256230144;T:638495895;N:84534", 75, 75, null, null, 451321309, 220819392, 256230144, 638495895, 84534, "SRX3856800", "SRS3100392", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.10189, 0.72988, 0.07219, 0.20488, 0.99281, 0.83899, 0.46012, 0.51971, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47904, "SRR6908712", "SRX3856800", "SRS3100392", "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.", null, "pubmed:31585086", null, "WKM5 unenriched", "GSM3070138", null, "tissue:WKM5 unenriched|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM5 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070138", "GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq", "GSM3070138", null, "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:GSM3070138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM5_unenriched_L004_R1_001.fastq.gz WKM5_unenriched_L004_R2_001.fastq.gz", "fastq fastq", 1470255063.0, 9745929.0, "GSM3070138 r4", "0:75.41 1:75.45", "A:425542718;C:206068561;G:242779977;T:595798063;N:65744", 75, 75, null, null, 425542718, 206068561, 242779977, 595798063, 65744, "SRX3856800", "SRS3100392", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.10318, 0.71368, 0.07165, 0.20008, 0.99159, 0.8508, 0.46642, 0.51043, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47909, "SRR6908701", "SRX3856798", "SRS3100390", "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.", null, "pubmed:31585086", null, "WKM5 hspcs", "GSM3070136", null, "tissue:WKM5 hspcs|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs", "WKM5 hspcs", "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 hspcs", null, "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", null, "FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs", "GSM3070136", "GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq", "GSM3070136", null, "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:GSM3070136", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM5_hspcs_L001_R2_001.fastq.gz WKM5_hspcs_L001_R1_001.fastq.gz", "fastq fastq", 6064422368.0, 40205564.0, "GSM3070136 r1", "0:75.42 1:75.41", "A:1792101497;C:906329224;G:1061291018;T:2303411628;N:1289001", 75, 75, null, null, 1792101497, 906329224, 1061291018, 2303411628, 1289001, "SRX3856798", "SRS3100390", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.07707, 0.61908, 0.04536, 0.14979, 0.98711, 0.86186, 0.54256, 0.52115, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47910, "SRR6908702", "SRX3856798", "SRS3100390", "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.", null, "pubmed:31585086", null, "WKM5 hspcs", "GSM3070136", null, "tissue:WKM5 hspcs|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs", "WKM5 hspcs", "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. 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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.", null, "pubmed:31585086", null, "WKM5 hspcs", "GSM3070136", null, "tissue:WKM5 hspcs|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs", "WKM5 hspcs", "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 hspcs", null, "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", null, "FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs", "GSM3070136", "GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq", "GSM3070136", null, "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:GSM3070136", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM5_hspcs_L003_R1_001.fastq.gz WKM5_hspcs_L003_R2_001.fastq.gz", "fastq fastq", 5866299339.0, 38885339.0, "GSM3070136 r3", "0:75.43 1:75.43", "A:1717556539;C:883848150;G:1028347614;T:2236229877;N:317159", 75, 75, null, null, 1717556539, 883848150, 1028347614, 2236229877, 317159, "SRX3856798", "SRS3100390", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.06878, 0.62531, 0.04189, 0.15336, 0.99113, 0.85888, 0.5, 0.51754, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47912, "SRR6908704", "SRX3856798", "SRS3100390", "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.", null, "pubmed:31585086", null, "WKM5 hspcs", "GSM3070136", null, "tissue:WKM5 hspcs|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs", "WKM5 hspcs", "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 hspcs", null, "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", null, "FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs", "GSM3070136", "GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq", "GSM3070136", null, "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:GSM3070136", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM5_hspcs_L004_R1_001.fastq.gz WKM5_hspcs_L004_R2_001.fastq.gz", "fastq fastq", 5566177327.0, 36895726.0, "GSM3070136 r4", "0:75.42 1:75.44", "A:1631791302;C:834536884;G:988788873;T:2110815191;N:245077", 75, 75, null, null, 1631791302, 834536884, 988788873, 2110815191, 245077, "SRX3856798", "SRS3100390", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.07494, 0.61393, 0.04705, 0.14806, 0.99032, 0.87178, 0.49704, 0.51802, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47913, "SRR6908697", "SRX3856797", "SRS3100389", "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.", null, "pubmed:31585086", null, "WKM4 unenriched", "GSM3070135", null, "tissue:WKM4 unenriched|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM4 unenriched", "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", "WKM4 unenriched", null, "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", null, "FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070135", "GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq", "GSM3070135", null, "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:GSM3070135", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM4_unenriched_L001_R2_001.fastq.gz WKM4_unenriched_L001_R1_001.fastq.gz", "fastq fastq", 1000182622.0, 6625590.0, "GSM3070135 r1", "0:75.50 1:75.46", "A:281062086;C:163533727;G:177503446;T:378045390;N:37973", 75, 75, null, null, 281062086, 163533727, 177503446, 378045390, 37973, "SRX3856797", "SRS3100389", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.32578, 0.64735, 0.27911, 0.49563, 0.94596, 0.8396, 0.51648, 0.52037, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47914, "SRR6908698", "SRX3856797", "SRS3100389", "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.", null, "pubmed:31585086", null, "WKM4 unenriched", "GSM3070135", null, "tissue:WKM4 unenriched|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM4 unenriched", "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", "WKM4 unenriched", null, "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", null, "FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070135", "GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq", "GSM3070135", null, "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:GSM3070135", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM4_unenriched_L002_R2_001.fastq.gz WKM4_unenriched_L002_R1_001.fastq.gz", "fastq fastq", 1024598143.0, 6787724.0, "GSM3070135 r2", "0:75.49 1:75.46", "A:287879816;C:166711858;G:184760618;T:385194933;N:50918", 75, 75, null, null, 287879816, 166711858, 184760618, 385194933, 50918, "SRX3856797", "SRS3100389", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.30906, 0.63868, 0.26505, 0.49323, 0.9498, 0.84977, 0.508, 0.53041, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47915, "SRR6908699", "SRX3856797", "SRS3100389", "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.", null, "pubmed:31585086", null, "WKM4 unenriched", "GSM3070135", null, "tissue:WKM4 unenriched|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM4 unenriched", "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", "WKM4 unenriched", null, "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", null, "FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070135", "GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq", "GSM3070135", null, "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:GSM3070135", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM4_unenriched_L003_R2_001.fastq.gz WKM4_unenriched_L003_R1_001.fastq.gz", "fastq fastq", 987354885.0, 6540694.0, "GSM3070135 r3", "0:75.50 1:75.46", "A:277978811;C:161185677;G:175345183;T:372839184;N:6030", 75, 75, null, null, 277978811, 161185677, 175345183, 372839184, 6030, "SRX3856797", "SRS3100389", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.32206, 0.64379, 0.27584, 0.49734, 0.94608, 0.84764, 0.51258, 0.52761, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47916, "SRR6908700", "SRX3856797", "SRS3100389", "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.", null, "pubmed:31585086", null, "WKM4 unenriched", "GSM3070135", null, "tissue:WKM4 unenriched|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM4 unenriched", "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", "WKM4 unenriched", null, "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", null, "FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070135", "GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq", "GSM3070135", null, "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:GSM3070135", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM4_unenriched_L004_R1_001.fastq.gz WKM4_unenriched_L004_R2_001.fastq.gz", "fastq fastq", 1001846281.0, 6636299.0, "GSM3070135 r4", "0:75.50 1:75.46", "A:280586899;C:163214034;G:180353077;T:377687027;N:5244", 75, 75, null, null, 280586899, 163214034, 180353077, 377687027, 5244, "SRX3856797", "SRS3100389", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.32088, 0.64536, 0.27364, 0.4929, 0.94663, 0.84822, 0.51406, 0.53384, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47921, "SRR6908689", "SRX3856795", "SRS3100387", "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.", null, "pubmed:31585086", null, "WKM3 unenriched", "GSM3070133", null, "tissue:WKM3 unenriched|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM3 unenriched", "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", "WKM3 unenriched", null, "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", null, "FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070133", "GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq", "GSM3070133", null, "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:GSM3070133", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM3_unenriched_L001_R1_001.fastq.gz WKM3_unenriched_L001_R2_001.fastq.gz", "fastq fastq", 1418323523.0, 9398733.0, "GSM3070133 r1", "0:75.43 1:75.47", "A:422643558;C:211337836;G:207870633;T:576229967;N:241529", 75, 75, null, null, 422643558, 211337836, 207870633, 576229967, 241529, "SRX3856795", "SRS3100387", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.38916, 0.82774, 0.31564, 0.36709, 0.96169, 0.9177, 0.50178, 0.54487, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47922, "SRR6908690", "SRX3856795", "SRS3100387", "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.", null, "pubmed:31585086", null, "WKM3 unenriched", "GSM3070133", null, "tissue:WKM3 unenriched|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM3 unenriched", "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", "WKM3 unenriched", null, "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", null, "FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070133", "GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq", "GSM3070133", null, "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:GSM3070133", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM3_unenriched_L002_R1_001.fastq.gz WKM3_unenriched_L002_R2_001.fastq.gz", "fastq fastq", 1297380885.0, 8597567.0, "GSM3070133 r2", "0:75.43 1:75.47", "A:384413707;C:192495936;G:194053875;T:526229304;N:188063", 75, 75, null, null, 384413707, 192495936, 194053875, 526229304, 188063, "SRX3856795", "SRS3100387", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.38661, 0.82306, 0.31693, 0.35768, 0.96171, 0.92468, 0.48342, 0.54858, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47923, "SRR6908691", "SRX3856795", "SRS3100387", "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.", null, "pubmed:31585086", null, "WKM3 unenriched", "GSM3070133", null, "tissue:WKM3 unenriched|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM3 unenriched", "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", "WKM3 unenriched", null, "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", null, "FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070133", "GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq", "GSM3070133", null, "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:GSM3070133", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM3_unenriched_L003_R1_001.fastq.gz WKM3_unenriched_L003_R2_001.fastq.gz", "fastq fastq", 1470091205.0, 9741084.0, "GSM3070133 r3", "0:75.44 1:75.48", "A:432738050;C:218429286;G:217928653;T:600846627;N:148589", 75, 75, null, null, 432738050, 218429286, 217928653, 600846627, 148589, "SRX3856795", "SRS3100387", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.39516, 0.83773, 0.32452, 0.36027, 0.96834, 0.91662, 0.49614, 0.5268, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47924, "SRR6908692", "SRX3856795", "SRS3100387", "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.", null, "pubmed:31585086", null, "WKM3 unenriched", "GSM3070133", null, "tissue:WKM3 unenriched|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM3 unenriched", "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", "WKM3 unenriched", null, "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", null, "FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070133", "GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq", "GSM3070133", null, "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:GSM3070133", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM3_unenriched_L004_R1_001.fastq.gz WKM3_unenriched_L004_R2_001.fastq.gz", "fastq fastq", 1400378972.0, 9280367.0, "GSM3070133 r4", "0:75.43 1:75.46", "A:412590948;C:206892406;G:210433218;T:570347127;N:115273", 75, 75, null, null, 412590948, 206892406, 210433218, 570347127, 115273, "SRX3856795", "SRS3100387", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.3812, 0.82835, 0.31027, 0.35634, 0.96889, 0.93608, 0.50533, 0.53883, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47933, "SRR6908677", "SRX3856791", "SRS3100383", "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.", null, "pubmed:31585086", null, "WKM2 unenriched", "GSM3070130", null, "tissue:WKM2 unenriched|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM2 unenriched", "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", "WKM2 unenriched", null, "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", null, "FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070130", "GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq", "GSM3070130", null, "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:GSM3070130", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM2_unenriched_L001_R2_001.fastq.gz WKM2_unenriched_L001_R1_001.fastq.gz", "fastq fastq", 1050338787.0, 6957998.0, "GSM3070130 r1", "0:75.46 1:75.50", "A:307962198;C:162998859;G:159301612;T:419897804;N:178314", 75, 75, null, null, 307962198, 162998859, 159301612, 419897804, 178314, "SRX3856791", "SRS3100383", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.40419, 0.79829, 0.34944, 0.46358, 0.95463, 0.92715, 0.5107, 0.52123, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47934, "SRR6908678", "SRX3856791", "SRS3100383", "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.", null, "pubmed:31585086", null, "WKM2 unenriched", "GSM3070130", null, "tissue:WKM2 unenriched|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM2 unenriched", "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", "WKM2 unenriched", null, "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", null, "FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070130", "GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq", "GSM3070130", null, "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:GSM3070130", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM2_unenriched_L002_R1_001.fastq.gz WKM2_unenriched_L002_R2_001.fastq.gz", "fastq fastq", 954172584.0, 6321045.0, "GSM3070130 r2", "0:75.45 1:75.50", "A:277724691;C:147647025;G:148192193;T:380472896;N:135779", 75, 75, null, null, 277724691, 147647025, 148192193, 380472896, 135779, "SRX3856791", "SRS3100383", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.40099, 0.79668, 0.34548, 0.45475, 0.95491, 0.93168, 0.512, 0.51844, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47935, "SRR6908679", "SRX3856791", "SRS3100383", "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.", null, "pubmed:31585086", null, "WKM2 unenriched", "GSM3070130", null, "tissue:WKM2 unenriched|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM2 unenriched", "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", "WKM2 unenriched", null, "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", null, "FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070130", "GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq", "GSM3070130", null, "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:GSM3070130", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM2_unenriched_L003_R1_001.fastq.gz WKM2_unenriched_L003_R2_001.fastq.gz", "fastq fastq", 1095988368.0, 7259975.0, "GSM3070130 r3", "0:75.47 1:75.50", "A:318145632;C:169141931;G:167581935;T:441001916;N:116954", 75, 75, null, null, 318145632, 169141931, 167581935, 441001916, 116954, "SRX3856791", "SRS3100383", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.4016, 0.81167, 0.34543, 0.45854, 0.96193, 0.92427, 0.51235, 0.51464, 76, 74, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47936, "SRR6908680", "SRX3856791", "SRS3100383", "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.", null, "pubmed:31585086", null, "WKM2 unenriched", "GSM3070130", null, "tissue:WKM2 unenriched|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM2 unenriched", "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", "WKM2 unenriched", null, "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", null, "FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070130", "GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq", "GSM3070130", null, "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:GSM3070130", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM2_unenriched_L004_R1_001.fastq.gz WKM2_unenriched_L004_R2_001.fastq.gz", "fastq fastq", 1028881429.0, 6816251.0, "GSM3070130 r4", "0:75.46 1:75.49", "A:298430122;C:158105868;G:160593676;T:411666228;N:85535", 75, 75, null, null, 298430122, 158105868, 160593676, 411666228, 85535, "SRX3856791", "SRS3100383", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.3924, 0.79036, 0.33854, 0.45285, 0.96386, 0.94568, 0.5146, 0.50952, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47945, "SRR6908665", "SRX3856788", "SRS3100380", "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.", null, "pubmed:31585086", null, "WKM1 unenriched and eosinphils", "GSM3070127", null, "tissue:WKM1 unenriched|FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM1 unenriched and eosinphils", "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", "WKM1 unenriched", null, "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", null, "FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070127", "GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq", "GSM3070127", null, "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:GSM3070127", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM1_unenriched_and_eosinphils_L001_R1_001.fastq.gz WKM1_unenriched_and_eosinphils_L001_R2_001.fastq.gz", "fastq fastq", 1068305818.0, 7080529.0, "GSM3070127 r1", "0:75.40 1:75.48", "A:320413848;C:151660462;G:160069867;T:435805461;N:356180", 75, 75, null, null, 320413848, 151660462, 160069867, 435805461, 356180, "SRX3856788", "SRS3100380", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.27598, 0.80871, 0.19091, 0.22599, 0.96861, 0.84488, 0.4721, 0.52448, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47946, "SRR6908666", "SRX3856788", "SRS3100380", "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.", null, "pubmed:31585086", null, "WKM1 unenriched and eosinphils", "GSM3070127", null, "tissue:WKM1 unenriched|FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM1 unenriched and eosinphils", "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", "WKM1 unenriched", null, "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", null, "FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070127", "GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq", "GSM3070127", null, "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:GSM3070127", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM1_unenriched_and_eosinphils_L002_R1_001.fastq.gz WKM1_unenriched_and_eosinphils_L002_R2_001.fastq.gz", "fastq fastq", 1016514463.0, 6737139.0, "GSM3070127 r2", "0:75.40 1:75.49", "A:302565774;C:144096988;G:155267617;T:414283021;N:301063", 75, 75, null, null, 302565774, 144096988, 155267617, 414283021, 301063, "SRX3856788", "SRS3100380", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.27295, 0.81917, 0.18669, 0.22848, 0.9668, 0.84587, 0.46708, 0.53709, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47947, "SRR6908667", "SRX3856788", "SRS3100380", "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.", null, "pubmed:31585086", null, "WKM1 unenriched and eosinphils", "GSM3070127", null, "tissue:WKM1 unenriched|FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM1 unenriched and eosinphils", "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", "WKM1 unenriched", null, "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", null, "FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070127", "GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq", "GSM3070127", null, "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:GSM3070127", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM1_unenriched_and_eosinphils_L003_R1_001.fastq.gz WKM1_unenriched_and_eosinphils_L003_R2_001.fastq.gz", "fastq fastq", 1086053144.0, 7197705.0, "GSM3070127 r3", "0:75.40 1:75.48", "A:318255993;C:154002465;G:165796480;T:447901015;N:97191", 75, 75, null, null, 318255993, 154002465, 165796480, 447901015, 97191, "SRX3856788", "SRS3100380", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.28052, 0.80997, 0.19564, 0.22597, 0.96765, 0.84254, 0.4696, 0.52611, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47948, "SRR6908668", "SRX3856788", "SRS3100380", "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.", null, "pubmed:31585086", null, "WKM1 unenriched and eosinphils", "GSM3070127", null, "tissue:WKM1 unenriched|FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM1 unenriched and eosinphils", "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", "WKM1 unenriched", null, "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", null, "FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070127", "GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq", "GSM3070127", null, "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:GSM3070127", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM1_unenriched_and_eosinphils_L004_R1_001.fastq.gz WKM1_unenriched_and_eosinphils_L004_R2_001.fastq.gz", "fastq fastq", 1085163813.0, 7191653.0, "GSM3070127 r4", "0:75.40 1:75.49", "A:312948861;C:153665711;G:169799718;T:448671627;N:77896", 75, 75, null, null, 312948861, 153665711, 169799718, 448671627, 77896, "SRX3856788", "SRS3100380", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.26916, 0.8114, 0.18523, 0.22636, 0.96627, 0.84354, 0.47209, 0.51851, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47949, "SRR6908659", "SRX3856787", "SRS3100379", "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.", null, "pubmed:31585086", null, "WKM10 unenriched", "GSM3070126", null, "tissue:WKM10 unenriched|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM10 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070126", "GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq", "GSM3070126", null, "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:GSM3070126", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM10_unenriched_L001_R1_001.fastq.gz WKM10_unenriched_L001_R2_001.fastq.gz", "fastq fastq", 1891142652.0, 12537041.0, "GSM3070126 r1", "0:75.42 1:75.42", "A:557482402;C:271919044;G:315036968;T:746296246;N:407992", 75, 75, null, null, 557482402, 271919044, 315036968, 746296246, 407992, "SRX3856787", "SRS3100379", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.16858, 0.70113, 0.12017, 0.25789, 0.98484, 0.84463, 0.51282, 0.51143, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47950, "SRR6908660", "SRX3856787", "SRS3100379", "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.", null, "pubmed:31585086", null, "WKM10 unenriched", "GSM3070126", null, "tissue:WKM10 unenriched|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM10 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070126", "GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq", "GSM3070126", null, "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:GSM3070126", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM10_unenriched_L002_R1_001.fastq.gz WKM10_unenriched_L002_R2_001.fastq.gz", "fastq fastq", 1846289680.0, 12239657.0, "GSM3070126 r2", "0:75.41 1:75.43", "A:544608247;C:262931581;G:312624132;T:725748545;N:377175", 75, 75, null, null, 544608247, 262931581, 312624132, 725748545, 377175, "SRX3856787", "SRS3100379", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.17135, 0.69505, 0.12425, 0.25051, 0.98466, 0.85401, 0.548, 0.50623, 76, 74, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47951, "SRR6908662", "SRX3856787", "SRS3100379", "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.", null, "pubmed:31585086", null, "WKM10 unenriched", "GSM3070126", null, "tissue:WKM10 unenriched|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM10 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070126", "GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq", "GSM3070126", null, "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:GSM3070126", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM10_unenriched_L003_R1_001.fastq.gz WKM10_unenriched_L003_R2_001.fastq.gz", "fastq fastq", 1832938497.0, 12149490.0, "GSM3070126 r3", "0:75.43 1:75.43", "A:535224222;C:265875558;G:305945153;T:725790414;N:103150", 75, 75, null, null, 535224222, 265875558, 305945153, 725790414, 103150, "SRX3856787", "SRS3100379", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.14834, 0.7084, 0.1064, 0.2628, 0.98884, 0.83997, 0.47131, 0.50686, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47952, "SRR6908663", "SRX3856787", "SRS3100379", "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.", null, "pubmed:31585086", null, "WKM10 unenriched", "GSM3070126", null, "tissue:WKM10 unenriched|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched", "WKM10 unenriched", "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 unenriched", null, "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", null, "FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070126", "GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq", "GSM3070126", null, "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:GSM3070126", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM10_unenriched_L004_R1_001.fastq.gz WKM10_unenriched_L004_R2_001.fastq.gz", "fastq fastq", 1728520288.0, 11457514.0, "GSM3070126 r4", "0:75.42 1:75.44", "A:506773176;C:249233970;G:290907978;T:681531010;N:74154", 75, 75, null, null, 506773176, 249233970, 290907978, 681531010, 74154, "SRX3856787", "SRS3100379", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.15928, 0.69759, 0.11494, 0.25416, 0.98748, 0.85257, 0.49753, 0.48714, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47957, "SRR6908651", "SRX3856785", "SRS3100378", "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.", null, "pubmed:31585086", null, "WKM10 hspcs", "GSM3070124", null, "tissue:WKM10 hspcs|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs", "WKM10 hspcs", "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 hspcs", null, "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", null, "FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs", "GSM3070124", "GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq", "GSM3070124", null, "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:GSM3070124", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM10_hspcs_L001_R2_001.fastq.gz WKM10_hspcs_L001_R1_001.fastq.gz", "fastq fastq", 1590301844.0, 10544259.0, "GSM3070124 r1", "0:75.41 1:75.41", "A:475941511;C:228957206;G:273207488;T:611864346;N:331293", 75, 75, null, null, 475941511, 228957206, 273207488, 611864346, 331293, "SRX3856785", "SRS3100378", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.1094, 0.64845, 0.07241, 0.20022, 0.99003, 0.86858, 0.47375, 0.52521, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47958, "SRR6908652", "SRX3856785", "SRS3100378", "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.", null, "pubmed:31585086", null, "WKM10 hspcs", "GSM3070124", null, "tissue:WKM10 hspcs|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs", "WKM10 hspcs", "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 hspcs", null, "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", null, "FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs", "GSM3070124", "GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq", "GSM3070124", null, "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:GSM3070124", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM10_hspcs_L002_R1_001.fastq.gz WKM10_hspcs_L002_R2_001.fastq.gz", "fastq fastq", 1541424200.0, 10220291.0, "GSM3070124 r2", "0:75.40 1:75.42", "A:461686116;C:219412558;G:269584176;T:590440374;N:300976", 75, 75, null, null, 461686116, 219412558, 269584176, 590440374, 300976, "SRX3856785", "SRS3100378", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.10207, 0.63661, 0.06952, 0.19781, 0.9906, 0.88067, 0.49271, 0.52658, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47959, "SRR6908653", "SRX3856785", "SRS3100378", "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.", null, "pubmed:31585086", null, "WKM10 hspcs", "GSM3070124", null, "tissue:WKM10 hspcs|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs", "WKM10 hspcs", "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 hspcs", null, "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", null, "FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs", "GSM3070124", "GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq", "GSM3070124", null, "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:GSM3070124", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM10_hspcs_L003_R1_001.fastq.gz WKM10_hspcs_L003_R2_001.fastq.gz", "fastq fastq", 1522328486.0, 10091828.0, "GSM3070124 r3", "0:75.42 1:75.42", "A:451216714;C:220917351;G:262800832;T:587312728;N:80861", 75, 75, null, null, 451216714, 220917351, 262800832, 587312728, 80861, "SRX3856785", "SRS3100378", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.13574, 0.65823, 0.09073, 0.20336, 0.99275, 0.86434, 0.43289, 0.52956, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47960, "SRR6908654", "SRX3856785", "SRS3100378", "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.", null, "pubmed:31585086", null, "WKM10 hspcs", "GSM3070124", null, "tissue:WKM10 hspcs|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs", "WKM10 hspcs", "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 hspcs", null, "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", null, "FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs", "GSM3070124", "GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq", "GSM3070124", null, "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:GSM3070124", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "WKM10_hspcs_L004_R1_001.fastq.gz WKM10_hspcs_L004_R2_001.fastq.gz", "fastq fastq", 1411385405.0, 9356766.0, "GSM3070124 r4", "0:75.41 1:75.43", "A:420850958;C:203157222;G:246195731;T:541125854;N:55640", 75, 75, null, null, 420850958, 203157222, 246195731, 541125854, 55640, "SRX3856785", "SRS3100378", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.1075, 0.63447, 0.07148, 0.19425, 0.99168, 0.87858, 0.46045, 0.52468, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47961, "SRR6908647", "SRX3856784", "SRS3100376", "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.", null, "pubmed:31585086", null, "TD2 unenriched6", "GSM3070123", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched6", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070123", "GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq", "GSM3070123", null, "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:GSM3070123", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched6_L001_R1_001.fastq.gz TD2_unenriched6_L001_R2_001.fastq.gz", "fastq fastq", 545810961.0, 3618641.0, "GSM3070123 r1", "0:75.34 1:75.49", "A:168172042;C:76647486;G:75443312;T:225350562;N:197559", 75, 75, null, null, 168172042, 76647486, 75443312, 225350562, 197559, "SRX3856784", "SRS3100376", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.21696, 0.7915, 0.16188, 0.2193, 0.99671, 0.95925, 0.45419, 0.56183, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47962, "SRR6908648", "SRX3856784", "SRS3100376", "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.", null, "pubmed:31585086", null, "TD2 unenriched6", "GSM3070123", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched6", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070123", "GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq", "GSM3070123", null, "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:GSM3070123", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched6_L002_R1_001.fastq.gz TD2_unenriched6_L002_R2_001.fastq.gz", "fastq fastq", 551469212.0, 3655214.0, "GSM3070123 r2", "0:75.36 1:75.52", "A:164774688;C:77140941;G:80606976;T:228739873;N:206734", 75, 75, null, null, 164774688, 77140941, 80606976, 228739873, 206734, "SRX3856784", "SRS3100376", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.19654, 0.81842, 0.14863, 0.22131, 0.99734, 0.94988, 0.44495, 0.52385, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47963, "SRR6908649", "SRX3856784", "SRS3100376", "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.", null, "pubmed:31585086", null, "TD2 unenriched6", "GSM3070123", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched6", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070123", "GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq", "GSM3070123", null, "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:GSM3070123", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched6_L003_R2_001.fastq.gz TD2_unenriched6_L003_R1_001.fastq.gz", "fastq fastq", 450161969.0, 2984169.0, "GSM3070123 r3", "0:75.35 1:75.50", "A:138199135;C:62817422;G:62600807;T:186468898;N:75707", 75, 75, null, null, 138199135, 62817422, 62600807, 186468898, 75707, "SRX3856784", "SRS3100376", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.21607, 0.79287, 0.16404, 0.21905, 0.99703, 0.95676, 0.48017, 0.55646, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47964, "SRR6908650", "SRX3856784", "SRS3100376", "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.", null, "pubmed:31585086", null, "TD2 unenriched6", "GSM3070123", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched6", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070123", "GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq", "GSM3070123", null, "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:GSM3070123", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched6_L004_R1_001.fastq.gz TD2_unenriched6_L004_R2_001.fastq.gz", "fastq fastq", 442656356.0, 2934612.0, "GSM3070123 r4", "0:75.33 1:75.51", "A:135781084;C:61366386;G:62664738;T:182773713;N:70435", 75, 75, null, null, 135781084, 61366386, 62664738, 182773713, 70435, "SRX3856784", "SRS3100376", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.18178, 0.75305, 0.13685, 0.21602, 0.99776, 0.9779, 0.4152, 0.56284, 76, 74, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47965, "SRR6908643", "SRX3856783", "SRS3100375", "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.", null, "pubmed:31585086", null, "TD2 unenriched5", "GSM3070122", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched5", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070122", "GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq", "GSM3070122", null, "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:GSM3070122", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched5_L001_R1_001.fastq.gz TD2_unenriched5_L001_R2_001.fastq.gz", "fastq fastq", 693452896.0, 4598401.0, "GSM3070122 r1", "0:75.33 1:75.48", "A:213825079;C:97881059;G:95953069;T:285544984;N:248705", 75, 75, null, null, 213825079, 97881059, 95953069, 285544984, 248705, "SRX3856783", "SRS3100375", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.16673, 0.76013, 0.12371, 0.17909, 0.99671, 0.95943, 0.51028, 0.50627, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47966, "SRR6908644", "SRX3856783", "SRS3100375", "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.", null, "pubmed:31585086", null, "TD2 unenriched5", "GSM3070122", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched5", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070122", "GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq", "GSM3070122", null, "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:GSM3070122", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched5_L002_R1_001.fastq.gz TD2_unenriched5_L002_R2_001.fastq.gz", "fastq fastq", 699177190.0, 4635107.0, "GSM3070122 r2", "0:75.34 1:75.50", "A:208880260;C:98335526;G:102541505;T:289154313;N:265586", 75, 75, null, null, 208880260, 98335526, 102541505, 289154313, 265586, "SRX3856783", "SRS3100375", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.16993, 0.79459, 0.12771, 0.18893, 0.99693, 0.94675, 0.4163, 0.53497, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47967, "SRR6908645", "SRX3856783", "SRS3100375", "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.", null, "pubmed:31585086", null, "TD2 unenriched5", "GSM3070122", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched5", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070122", "GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq", "GSM3070122", null, "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:GSM3070122", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched5_L003_R1_001.fastq.gz TD2_unenriched5_L003_R2_001.fastq.gz", "fastq fastq", 576884372.0, 3824943.0, "GSM3070122 r3", "0:75.33 1:75.49", "A:177240215;C:80846391;G:80350870;T:238347702;N:99194", 75, 75, null, null, 177240215, 80846391, 80350870, 238347702, 99194, "SRX3856783", "SRS3100375", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.16558, 0.7756, 0.12819, 0.17822, 0.99709, 0.95432, 0.42857, 0.53851, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47968, "SRR6908646", "SRX3856783", "SRS3100375", "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.", null, "pubmed:31585086", null, "TD2 unenriched5", "GSM3070122", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched5", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070122", "GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq", "GSM3070122", null, "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:GSM3070122", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched5_L004_R1_001.fastq.gz TD2_unenriched5_L004_R2_001.fastq.gz", "fastq fastq", 576258135.0, 3821008.0, "GSM3070122 r4", "0:75.32 1:75.49", "A:176675655;C:80188796;G:82006998;T:237292671;N:94015", 75, 75, null, null, 176675655, 80188796, 82006998, 237292671, 94015, "SRX3856783", "SRS3100375", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.14911, 0.72985, 0.12068, 0.18331, 0.99831, 0.97735, 0.4031, 0.53561, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47969, "SRR6908639", "SRX3856782", "SRS3100374", "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.", null, "pubmed:31585086", null, "TD2 unenriched4", "GSM3070121", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched4", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070121", "GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq", "GSM3070121", null, "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:GSM3070121", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched4_L001_R1_001.fastq.gz TD2_unenriched4_L001_R2_001.fastq.gz", "fastq fastq", 698012656.0, 4628160.0, "GSM3070121 r1", "0:75.33 1:75.49", "A:215875472;C:99834912;G:97411477;T:284642018;N:248777", 75, 75, null, null, 215875472, 99834912, 97411477, 284642018, 248777, "SRX3856782", "SRS3100374", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.13242, 0.78521, 0.09514, 0.21281, 0.99695, 0.96187, 0.55958, 0.54425, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47970, "SRR6908640", "SRX3856782", "SRS3100374", "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.", null, "pubmed:31585086", null, "TD2 unenriched4", "GSM3070121", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched4", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070121", "GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq", "GSM3070121", null, "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:GSM3070121", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched4_L002_R1_001.fastq.gz TD2_unenriched4_L002_R2_001.fastq.gz", "fastq fastq", 700004319.0, 4640053.0, "GSM3070121 r2", "0:75.35 1:75.52", "A:209624561;C:99781032;G:103500007;T:286831762;N:266957", 75, 75, null, null, 209624561, 99781032, 103500007, 286831762, 266957, "SRX3856782", "SRS3100374", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.13829, 0.81458, 0.10266, 0.21216, 0.99687, 0.94913, 0.54395, 0.53632, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47971, "SRR6908641", "SRX3856782", "SRS3100374", "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.", null, "pubmed:31585086", null, "TD2 unenriched4", "GSM3070121", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched4", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070121", "GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq", "GSM3070121", null, "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:GSM3070121", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched4_L003_R1_001.fastq.gz TD2_unenriched4_L003_R2_001.fastq.gz", "fastq fastq", 574436722.0, 3808300.0, "GSM3070121 r3", "0:75.34 1:75.50", "A:177021417;C:81616991;G:80653244;T:235045589;N:99481", 75, 75, null, null, 177021417, 81616991, 80653244, 235045589, 99481, "SRX3856782", "SRS3100374", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.12255, 0.79777, 0.09509, 0.21314, 0.99772, 0.95735, 0.44927, 0.54033, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47972, "SRR6908642", "SRX3856782", "SRS3100374", "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.", null, "pubmed:31585086", null, "TD2 unenriched4", "GSM3070121", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched4", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070121", "GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq", "GSM3070121", null, "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:GSM3070121", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched4_L004_R1_001.fastq.gz TD2_unenriched4_L004_R2_001.fastq.gz", "fastq fastq", 569447738.0, 3775476.0, "GSM3070121 r4", "0:75.32 1:75.51", "A:175211390;C:80267913;G:81642398;T:232235494;N:90543", 75, 75, null, null, 175211390, 80267913, 81642398, 232235494, 90543, "SRX3856782", "SRS3100374", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.12315, 0.75952, 0.09398, 0.20424, 0.99784, 0.97788, 0.46825, 0.56598, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47973, "SRR6908635", "SRX3856781", "SRS3100373", "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.", null, "pubmed:31585086", null, "TD2 unenriched3", "GSM3070120", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched3", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070120", "GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq", "GSM3070120", null, "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:GSM3070120", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched3_L001_R1_001.fastq.gz TD2_unenriched3_L001_R2_001.fastq.gz", "fastq fastq", 1064615599.0, 7058899.0, "GSM3070120 r1", "0:75.33 1:75.49", "A:331155753;C:152195592;G:149457994;T:431416903;N:389357", 75, 75, null, null, 331155753, 152195592, 149457994, 431416903, 389357, "SRX3856781", "SRS3100373", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.12965, 0.76924, 0.09102, 0.22546, 0.99693, 0.95895, 0.46568, 0.56174, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47974, "SRR6908636", "SRX3856781", "SRS3100373", "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.", null, "pubmed:31585086", null, "TD2 unenriched3", "GSM3070120", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched3", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070120", "GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq", "GSM3070120", null, "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:GSM3070120", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched3_L002_R1_001.fastq.gz TD2_unenriched3_L002_R2_001.fastq.gz", "fastq fastq", 1070747888.0, 7097567.0, "GSM3070120 r2", "0:75.35 1:75.51", "A:322612282;C:152497154;G:159486633;T:435752070;N:399749", 75, 75, null, null, 322612282, 152497154, 159486633, 435752070, 399749, "SRX3856781", "SRS3100373", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.11805, 0.79563, 0.08703, 0.22302, 0.99738, 0.94838, 0.49404, 0.53615, 75, 74, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47975, "SRR6908637", "SRX3856781", "SRS3100373", "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.", null, "pubmed:31585086", null, "TD2 unenriched3", "GSM3070120", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched3", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070120", "GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq", "GSM3070120", null, "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:GSM3070120", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched3_L003_R1_001.fastq.gz TD2_unenriched3_L003_R2_001.fastq.gz", "fastq fastq", 886095506.0, 5874463.0, "GSM3070120 r3", "0:75.34 1:75.50", "A:274560800;C:125930642;G:125194660;T:360267888;N:141516", 75, 75, null, null, 274560800, 125930642, 125194660, 360267888, 141516, "SRX3856781", "SRS3100373", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.11795, 0.77243, 0.08536, 0.2207, 0.99752, 0.95554, 0.48447, 0.53023, 74, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47976, "SRR6908638", "SRX3856781", "SRS3100373", "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.", null, "pubmed:31585086", null, "TD2 unenriched3", "GSM3070120", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched3", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070120", "GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq", "GSM3070120", null, "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:GSM3070120", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched3_L004_R1_001.fastq.gz TD2_unenriched3_L004_R2_001.fastq.gz", "fastq fastq", 886839338.0, 5879735.0, "GSM3070120 r4", "0:75.33 1:75.50", "A:274032562;C:125082235;G:128147333;T:359436665;N:140543", 75, 75, null, null, 274032562, 125082235, 128147333, 359436665, 140543, "SRX3856781", "SRS3100373", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.10406, 0.73196, 0.07637, 0.22039, 0.99805, 0.97806, 0.57024, 0.5327, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47977, "SRR6908631", "SRX3856780", "SRS3100372", "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.", null, "pubmed:31585086", null, "TD2 unenriched2", "GSM3070119", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched2", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070119", "GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq", "GSM3070119", null, "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:GSM3070119", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched2_L001_R2_001.fastq.gz TD2_unenriched2_L001_R1_001.fastq.gz", "fastq fastq", 704234076.0, 4666720.0, "GSM3070119 r1", "0:75.40 1:75.51", "A:214197936;C:98747742;G:99261324;T:291802858;N:224216", 75, 75, null, null, 214197936, 98747742, 99261324, 291802858, 224216, "SRX3856780", "SRS3100372", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.35492, 0.86117, 0.25299, 0.26523, 0.97461, 0.90398, 0.48193, 0.51578, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47978, "SRR6908632", "SRX3856780", "SRS3100372", "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.", null, "pubmed:31585086", null, "TD2 unenriched2", "GSM3070119", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched2", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070119", "GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq", "GSM3070119", null, "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:GSM3070119", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched2_L002_R1_001.fastq.gz TD2_unenriched2_L002_R2_001.fastq.gz", "fastq fastq", 765278281.0, 5071250.0, "GSM3070119 r2", "0:75.39 1:75.51", "A:229620635;C:106485326;G:110950848;T:318002131;N:219341", 75, 75, null, null, 229620635, 106485326, 110950848, 318002131, 219341, "SRX3856780", "SRS3100372", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.34672, 0.85932, 0.24701, 0.26154, 0.97309, 0.90404, 0.44868, 0.53509, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47979, "SRR6908633", "SRX3856780", "SRS3100372", "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.", null, "pubmed:31585086", null, "TD2 unenriched2", "GSM3070119", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched2", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070119", "GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq", "GSM3070119", null, "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:GSM3070119", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched2_L003_R2_001.fastq.gz TD2_unenriched2_L003_R1_001.fastq.gz", "fastq fastq", 687934305.0, 4558488.0, "GSM3070119 r3", "0:75.41 1:75.51", "A:206475938;C:96511863;G:97660355;T:287209767;N:76382", 75, 75, null, null, 206475938, 96511863, 97660355, 287209767, 76382, "SRX3856780", "SRS3100372", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.36436, 0.861, 0.2595, 0.26448, 0.97699, 0.90772, 0.47159, 0.5237, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47980, "SRR6908634", "SRX3856780", "SRS3100372", "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.", null, "pubmed:31585086", null, "TD2 unenriched2", "GSM3070119", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched2", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070119", "GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq", "GSM3070119", null, "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:GSM3070119", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched2_L004_R2_001.fastq.gz TD2_unenriched2_L004_R1_001.fastq.gz", "fastq fastq", 726529569.0, 4814235.0, "GSM3070119 r4", "0:75.40 1:75.51", "A:216493809;C:101292463;G:105024164;T:303652778;N:66355", 75, 75, null, null, 216493809, 101292463, 105024164, 303652778, 66355, "SRX3856780", "SRS3100372", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.35832, 0.85478, 0.25668, 0.26566, 0.97786, 0.9232, 0.43793, 0.51027, 75, 74, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47981, "SRR6908627", "SRX3856779", "SRS3100371", "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.", null, "pubmed:31585086", null, "TD2 unenriched1", "GSM3070118", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched1", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070118", "GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq", "GSM3070118", null, "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:GSM3070118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched1_L001_R1_001.fastq.gz TD2_unenriched1_L001_R2_001.fastq.gz", "fastq fastq", 854990718.0, 5665060.0, "GSM3070118 r1", "0:75.41 1:75.52", "A:254734570;C:122614765;G:124439336;T:352929607;N:272440", 75, 75, null, null, 254734570, 122614765, 124439336, 352929607, 272440, "SRX3856779", "SRS3100371", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.36338, 0.86281, 0.26887, 0.24825, 0.97011, 0.88966, 0.52127, 0.54178, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47982, "SRR6908628", "SRX3856779", "SRS3100371", "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.", null, "pubmed:31585086", null, "TD2 unenriched1", "GSM3070118", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched1", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070118", "GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq", "GSM3070118", null, "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:GSM3070118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched1_L002_R1_001.fastq.gz TD2_unenriched1_L002_R2_001.fastq.gz", "fastq fastq", 930416984.0, 6164856.0, "GSM3070118 r2", "0:75.40 1:75.52", "A:273371770;C:132477140;G:139134453;T:385153908;N:279713", 75, 75, null, null, 273371770, 132477140, 139134453, 385153908, 279713, "SRX3856779", "SRS3100371", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.35067, 0.86515, 0.25837, 0.24485, 0.97041, 0.88838, 0.50653, 0.5351, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47983, "SRR6908629", "SRX3856779", "SRS3100371", "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.", null, "pubmed:31585086", null, "TD2 unenriched1", "GSM3070118", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched1", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070118", "GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq", "GSM3070118", null, "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:GSM3070118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched1_L003_R1_001.fastq.gz TD2_unenriched1_L003_R2_001.fastq.gz", "fastq fastq", 854585314.0, 5662042.0, "GSM3070118 r3", "0:75.42 1:75.52", "A:251015969;C:122655652;G:125410058;T:355402307;N:101328", 75, 75, null, null, 251015969, 122655652, 125410058, 355402307, 101328, "SRX3856779", "SRS3100371", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.37061, 0.86557, 0.27852, 0.24591, 0.97498, 0.89335, 0.49141, 0.48962, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47984, "SRR6908630", "SRX3856779", "SRS3100371", "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.", null, "pubmed:31585086", null, "TD2 unenriched1", "GSM3070118", null, "tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD2 unenriched1", "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", "TD2 unenriched", null, "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", null, "FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070118", "GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq", "GSM3070118", null, "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:GSM3070118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD2_unenriched1_L004_R1_001.fastq.gz TD2_unenriched1_L004_R2_001.fastq.gz", "fastq fastq", 886769985.0, 5875288.0, "GSM3070118 r4", "0:75.41 1:75.52", "A:258347255;C:126714596;G:132415950;T:369203307;N:88877", 75, 75, null, null, 258347255, 126714596, 132415950, 369203307, 88877, "SRX3856779", "SRS3100371", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.36759, 0.86048, 0.27631, 0.23985, 0.97526, 0.90682, 0.49809, 0.53286, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47985, "SRR6908623", "SRX3856778", "SRS3100370", "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.", null, "pubmed:31585086", null, "TD1c unenriched2", "GSM3070117", null, "tissue:TD1c unenriched|FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1c unenriched2", "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", "TD1c unenriched", null, "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", null, "FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070117", "GSM3070117: TD1c unenriched2; Danio rerio; RNA Seq", "GSM3070117", null, "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:GSM3070117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1c_unenriched2_L001_R2_001.fastq.gz TD1c_unenriched2_L001_R1_001.fastq.gz", "fastq fastq", 1102562702.0, 7312561.0, "GSM3070117 r1", "0:75.35 1:75.42", "A:335758641;C:142453672;G:147050519;T:476966325;N:333545", 75, 75, null, null, 335758641, 142453672, 147050519, 476966325, 333545, "SRX3856778", "SRS3100370", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.18873, 0.85606, 0.15715, 0.20503, 0.99389, 0.89219, 0.38461, 0.52785, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47986, "SRR6908624", "SRX3856778", "SRS3100370", "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.", null, "pubmed:31585086", null, "TD1c unenriched2", "GSM3070117", null, "tissue:TD1c unenriched|FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1c unenriched2", "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", "TD1c unenriched", null, "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", null, "FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070117", "GSM3070117: TD1c unenriched2; Danio rerio; RNA Seq", "GSM3070117", null, "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:GSM3070117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1c_unenriched2_L002_R2_001.fastq.gz TD1c_unenriched2_L002_R1_001.fastq.gz", "fastq fastq", 1076269826.0, 7138199.0, "GSM3070117 r2", "0:75.36 1:75.42", "A:327735681;C:138132014;G:146113752;T:463938511;N:349868", 75, 75, null, null, 327735681, 138132014, 146113752, 463938511, 349868, "SRX3856778", "SRS3100370", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.18581, 0.85373, 0.15134, 0.20593, 0.99417, 0.89903, 0.40125, 0.53405, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47987, "SRR6908625", "SRX3856778", "SRS3100370", "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.", null, "pubmed:31585086", null, "TD1c unenriched2", "GSM3070117", null, "tissue:TD1c unenriched|FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1c unenriched2", "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", "TD1c unenriched", null, "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", null, "FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070117", "GSM3070117: TD1c unenriched2; Danio rerio; RNA Seq", "GSM3070117", null, "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:GSM3070117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1c_unenriched2_L003_R1_001.fastq.gz TD1c_unenriched2_L003_R2_001.fastq.gz", "fastq fastq", 975975770.0, 6472365.0, "GSM3070117 r3", "0:75.37 1:75.42", "A:296078451;C:125094164;G:131703273;T:423017614;N:82268", 75, 75, null, null, 296078451, 125094164, 131703273, 423017614, 82268, "SRX3856778", "SRS3100370", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.18767, 0.85545, 0.1562, 0.20405, 0.99472, 0.8929, 0.39444, 0.55292, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47988, "SRR6908626", "SRX3856778", "SRS3100370", "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.", null, "pubmed:31585086", null, "TD1c unenriched2", "GSM3070117", null, "tissue:TD1c unenriched|FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1c unenriched2", "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", "TD1c unenriched", null, "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", null, "FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070117", "GSM3070117: TD1c unenriched2; Danio rerio; RNA Seq", "GSM3070117", null, "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:GSM3070117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1c_unenriched2_L004_R1_001.fastq.gz TD1c_unenriched2_L004_R2_001.fastq.gz", "fastq fastq", 933773638.0, 6193771.0, "GSM3070117 r4", "0:75.37 1:75.39", "A:282973758;C:119502214;G:126826686;T:404378027;N:92953", 75, 75, null, null, 282973758, 119502214, 126826686, 404378027, 92953, "SRX3856778", "SRS3100370", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.17755, 0.85124, 0.15014, 0.20728, 0.99573, 0.90709, 0.37372, 0.567, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47989, "SRR6908619", "SRX3856777", "SRS3100369", "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.", null, "pubmed:31585086", null, "TD1c unenriched1", "GSM3070116", null, "tissue:TD1c unenriched|FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1c unenriched1", "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", "TD1c unenriched", null, "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", null, "FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070116", "GSM3070116: TD1c unenriched1; Danio rerio; RNA Seq", "GSM3070116", null, "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:GSM3070116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1c_unenriched1_L001_R1_001.fastq.gz TD1c_unenriched1_L001_R2_001.fastq.gz", "fastq fastq", 1031608750.0, 6842181.0, "GSM3070116 r1", "0:75.35 1:75.42", "A:311429598;C:133326447;G:138966281;T:447588072;N:298352", 75, 75, null, null, 311429598, 133326447, 138966281, 447588072, 298352, "SRX3856777", "SRS3100369", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.18592, 0.86268, 0.15126, 0.15242, 0.99403, 0.89073, 0.34842, 0.51976, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47990, "SRR6908620", "SRX3856777", "SRS3100369", "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.", null, "pubmed:31585086", null, "TD1c unenriched1", "GSM3070116", null, "tissue:TD1c unenriched|FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1c unenriched1", "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", "TD1c unenriched", null, "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", null, "FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070116", "GSM3070116: TD1c unenriched1; Danio rerio; RNA Seq", "GSM3070116", null, "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:GSM3070116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1c_unenriched1_L002_R1_001.fastq.gz TD1c_unenriched1_L002_R2_001.fastq.gz", "fastq fastq", 991734477.0, 6577784.0, "GSM3070116 r2", "0:75.35 1:75.42", "A:299336642;C:127159354;G:135832175;T:429079031;N:327275", 75, 75, null, null, 299336642, 127159354, 135832175, 429079031, 327275, "SRX3856777", "SRS3100369", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.18256, 0.86084, 0.14862, 0.15148, 0.99421, 0.89554, 0.37277, 0.52142, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47991, "SRR6908621", "SRX3856777", "SRS3100369", "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.", null, "pubmed:31585086", null, "TD1c unenriched1", "GSM3070116", null, "tissue:TD1c unenriched|FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1c unenriched1", "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", "TD1c unenriched", null, "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", null, "FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070116", "GSM3070116: TD1c unenriched1; Danio rerio; RNA Seq", "GSM3070116", null, "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:GSM3070116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1c_unenriched1_L003_R1_001.fastq.gz TD1c_unenriched1_L003_R2_001.fastq.gz", "fastq fastq", 893273550.0, 5924156.0, "GSM3070116 r3", "0:75.36 1:75.42", "A:268855509;C:114591509;G:121619518;T:388130959;N:76055", 75, 75, null, null, 268855509, 114591509, 121619518, 388130959, 76055, "SRX3856777", "SRS3100369", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.18423, 0.86371, 0.1536, 0.1499, 0.995, 0.88832, 0.36027, 0.54585, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47992, "SRR6908622", "SRX3856777", "SRS3100369", "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.", null, "pubmed:31585086", null, "TD1c unenriched1", "GSM3070116", null, "tissue:TD1c unenriched|FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1c unenriched1", "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", "TD1c unenriched", null, "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", null, "FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070116", "GSM3070116: TD1c unenriched1; Danio rerio; RNA Seq", "GSM3070116", null, "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:GSM3070116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1c_unenriched1_L004_R1_001.fastq.gz TD1c_unenriched1_L004_R2_001.fastq.gz", "fastq fastq", 839401139.0, 5567966.0, "GSM3070116 r4", "0:75.36 1:75.39", "A:252017893;C:107009489;G:115098370;T:365192003;N:83384", 75, 75, null, null, 252017893, 107009489, 115098370, 365192003, 83384, "SRX3856777", "SRS3100369", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.1828, 0.85796, 0.15374, 0.1507, 0.9959, 0.90563, 0.37155, 0.5635, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47993, "SRR6908615", "SRX3856776", "SRS3100368", "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.", null, "pubmed:31585086", null, "TD1b unenriched2", "GSM3070115", null, "tissue:TD1b unenriched|FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1b unenriched2", "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", "TD1b unenriched", null, "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", null, "FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070115", "GSM3070115: TD1b unenriched2; Danio rerio; RNA Seq", "GSM3070115", null, "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:GSM3070115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1b_unenriched2_L001_R2_001.fastq.gz TD1b_unenriched2_L001_R1_001.fastq.gz", "fastq fastq", 1289477359.0, 8541020.0, "GSM3070115 r1", "0:75.47 1:75.51", "A:337226443;C:189301381;G:198668726;T:564273181;N:7628", 75, 75, null, null, 337226443, 189301381, 198668726, 564273181, 7628, "SRX3856776", "SRS3100368", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.22254, 0.90113, 0.16689, 0.25348, 0.99421, 0.86858, 0.3644, 0.53872, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47994, "SRR6908616", "SRX3856776", "SRS3100368", "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.", null, "pubmed:31585086", null, "TD1b unenriched2", "GSM3070115", null, "tissue:TD1b unenriched|FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1b unenriched2", "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", "TD1b unenriched", null, "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", null, "FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070115", "GSM3070115: TD1b unenriched2; Danio rerio; RNA Seq", "GSM3070115", null, "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:GSM3070115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1b_unenriched2_L002_R1_001.fastq.gz TD1b_unenriched2_L002_R2_001.fastq.gz", "fastq fastq", 1322667792.0, 8760602.0, "GSM3070115 r2", "0:75.47 1:75.51", "A:344650470;C:194854498;G:204129732;T:579029173;N:3919", 75, 75, null, null, 344650470, 194854498, 204129732, 579029173, 3919, "SRX3856776", "SRS3100368", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.21366, 0.90126, 0.16079, 0.25304, 0.99464, 0.86803, 0.3734, 0.53564, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47995, "SRR6908617", "SRX3856776", "SRS3100368", "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.", null, "pubmed:31585086", null, "TD1b unenriched2", "GSM3070115", null, "tissue:TD1b unenriched|FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1b unenriched2", "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", "TD1b unenriched", null, "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", null, "FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070115", "GSM3070115: TD1b unenriched2; Danio rerio; RNA Seq", "GSM3070115", null, "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:GSM3070115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1b_unenriched2_L003_R1_001.fastq.gz TD1b_unenriched2_L003_R2_001.fastq.gz", "fastq fastq", 1212594351.0, 8031993.0, "GSM3070115 r3", "0:75.46 1:75.51", "A:316565624;C:177071026;G:186626042;T:532324002;N:7657", 75, 75, null, null, 316565624, 177071026, 186626042, 532324002, 7657, "SRX3856776", "SRS3100368", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.23021, 0.90115, 0.17997, 0.25341, 0.99602, 0.86821, 0.31011, 0.53374, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47996, "SRR6908618", "SRX3856776", "SRS3100368", "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.", null, "pubmed:31585086", null, "TD1b unenriched2", "GSM3070115", null, "tissue:TD1b unenriched|FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1b unenriched2", "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", "TD1b unenriched", null, "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", null, "FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070115", "GSM3070115: TD1b unenriched2; Danio rerio; RNA Seq", "GSM3070115", null, "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:GSM3070115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1b_unenriched2_L004_R1_001.fastq.gz TD1b_unenriched2_L004_R2_001.fastq.gz", "fastq fastq", 1233997259.0, 8173463.0, "GSM3070115 r4", "0:75.47 1:75.51", "A:321641054;C:181327208;G:189853023;T:541174134;N:1840", 75, 75, null, null, 321641054, 181327208, 189853023, 541174134, 1840, "SRX3856776", "SRS3100368", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.20874, 0.90009, 0.16567, 0.25552, 0.9964, 0.87176, 0.33252, 0.53155, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47997, "SRR6908610", "SRX3856775", "SRS3100367", "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.", null, "pubmed:31585086", null, "TD1b unenriched1", "GSM3070114", null, "tissue:TD1b unenriched|FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1b unenriched1", "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", "TD1b unenriched", null, "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", null, "FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070114", "GSM3070114: TD1b unenriched1; Danio rerio; RNA Seq", "GSM3070114", null, "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:GSM3070114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1b_unenriched1_L001_R1_001.fastq.gz TD1b_unenriched1_L001_R2_001.fastq.gz", "fastq fastq", 1214668085.0, 8046150.0, "GSM3070114 r1", "0:75.46 1:75.50", "A:317548560;C:178894444;G:189532433;T:528685664;N:6984", 75, 75, null, null, 317548560, 178894444, 189532433, 528685664, 6984, "SRX3856775", "SRS3100367", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.2025, 0.89826, 0.15463, 0.24447, 0.99397, 0.85849, 0.37003, 0.53443, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47998, "SRR6908611", "SRX3856775", "SRS3100367", "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.", null, "pubmed:31585086", null, "TD1b unenriched1", "GSM3070114", null, "tissue:TD1b unenriched|FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1b unenriched1", "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", "TD1b unenriched", null, "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", null, "FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070114", "GSM3070114: TD1b unenriched1; Danio rerio; RNA Seq", "GSM3070114", null, "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:GSM3070114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, "TD1b_unenriched1_L002_R1_001.fastq.gz TD1b_unenriched1_L002_R2_001.fastq.gz", "fastq fastq", 1243396410.0, 8236168.0, "GSM3070114 r2", "0:75.46 1:75.50", "A:323654814;C:183830040;G:194411746;T:541496602;N:3208", 75, 75, null, null, 323654814, 183830040, 194411746, 541496602, 3208, "SRX3856775", "SRS3100367", "SRA675960", "GEO", "Hubrecht Institute", 2, 0.19621, 0.89856, 0.147, 0.24547, 0.99393, 0.85999, 0.42201, 0.5295, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-03-28", "Undetermined", "Undetermined", "Kidney", "Renal System"], [47999, "SRR6908613", "SRX3856775", "SRS3100367", "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.", null, "pubmed:31585086", null, "TD1b unenriched1", "GSM3070114", null, "tissue:TD1b unenriched|FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1b unenriched1", "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. 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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.", null, "pubmed:31585086", null, "TD1b unenriched1", "GSM3070114", null, "tissue:TD1b unenriched|FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "TD1b unenriched1", "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", "TD1b unenriched", null, "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", null, "FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched", "GSM3070114", "GSM3070114: TD1b unenriched1; Danio rerio; RNA Seq", "GSM3070114", null, "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:GSM3070114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP136633", null, null, 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"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"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], 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