rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 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.,,pubmed:31585086,,WKM9 unenriched,GSM3070148,,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. 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 unenriched,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070148,GSM3070148: WKM9 unenriched; Danio rerio; RNA Seq,GSM3070148,,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:GSM3070148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_unenriched_L001_R1_001.fastq.gz WKM9_unenriched_L001_R2_001.fastq.gz,fastq fastq,1346805481.0,8925729.0,GSM3070148 r1,0:75.41 1:75.48,A:389424098;C:209314278;G:233588167;T:514471922;N:7016,75,75,,,389424098,209314278,233588167,514471922,7016,SRX3856810,SRS3100403,SRA675960,GEO,Hubrecht Institute,2,0.43527,0.79133,0.35777,0.52091,0.95361,0.87156,0.48343,0.54164,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System 47862,SRR6908752,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.,,pubmed:31585086,,WKM9 unenriched,GSM3070148,,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. 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 unenriched,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070148,GSM3070148: WKM9 unenriched; Danio rerio; RNA Seq,GSM3070148,,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:GSM3070148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_unenriched_L002_R1_001.fastq.gz WKM9_unenriched_L002_R2_001.fastq.gz,fastq fastq,1325332076.0,8783303.0,GSM3070148 r2,0:75.41 1:75.48,A:380077587;C:204687058;G:234896688;T:505666915;N:3828,75,75,,,380077587,204687058,234896688,505666915,3828,SRX3856810,SRS3100403,SRA675960,GEO,Hubrecht Institute,2,0.42931,0.78191,0.35315,0.51028,0.95787,0.87493,0.49522,0.49685,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System 47863,SRR6908753,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.,,pubmed:31585086,,WKM9 unenriched,GSM3070148,,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. 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 unenriched,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070148,GSM3070148: WKM9 unenriched; Danio rerio; RNA Seq,GSM3070148,,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:GSM3070148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_unenriched_L003_R1_001.fastq.gz WKM9_unenriched_L003_R2_001.fastq.gz,fastq fastq,1209174922.0,8013226.0,GSM3070148 r3,0:75.42 1:75.47,A:347525516;C:187142186;G:212384943;T:462099359;N:22918,75,75,,,347525516,187142186,212384943,462099359,22918,SRX3856810,SRS3100403,SRA675960,GEO,Hubrecht Institute,2,0.4232,0.78709,0.34991,0.51583,0.9614,0.88215,0.50753,0.49857,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System 47864,SRR6908754,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.,,pubmed:31585086,,WKM9 unenriched,GSM3070148,,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. 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 unenriched,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070148,GSM3070148: WKM9 unenriched; Danio rerio; RNA Seq,GSM3070148,,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:GSM3070148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_unenriched_L004_R1_001.fastq.gz WKM9_unenriched_L004_R2_001.fastq.gz,fastq fastq,1177710986.0,7804805.0,GSM3070148 r4,0:75.42 1:75.47,A:337640779;C:180611864;G:209653010;T:449785638;N:19695,75,75,,,337640779,180611864,209653010,449785638,19695,SRX3856810,SRS3100403,SRA675960,GEO,Hubrecht Institute,2,0.42938,0.78452,0.35813,0.51351,0.96435,0.89035,0.46765,0.55409,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System 47865,SRR6908747,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.,,pubmed:31585086,,WKM9 monocytes,GSM3070147,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070147,GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq,GSM3070147,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM9 monocytes,GSM3070147,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070147,GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq,GSM3070147,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM9 monocytes,GSM3070147,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070147,GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq,GSM3070147,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM9 monocytes,GSM3070147,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070147,GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq,GSM3070147,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM8 unenriched,GSM3070145,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070145,GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq,GSM3070145,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM8 unenriched,GSM3070145,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070145,GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq,GSM3070145,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM8 unenriched,GSM3070145,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070145,GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq,GSM3070145,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM8 unenriched,GSM3070145,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070145,GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq,GSM3070145,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM8 monocytes,GSM3070144,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070144,GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq,GSM3070144,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM8 monocytes,GSM3070144,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070144,GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq,GSM3070144,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM8 monocytes,GSM3070144,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070144,GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq,GSM3070144,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM8 monocytes,GSM3070144,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070144,GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq,GSM3070144,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM7 unenriched,GSM3070142,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070142,GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq,GSM3070142,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM7 unenriched,GSM3070142,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070142,GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq,GSM3070142,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM7 unenriched,GSM3070142,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070142,GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq,GSM3070142,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM7 unenriched,GSM3070142,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070142,GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq,GSM3070142,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM7 monocytes,GSM3070141,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070141,GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq,GSM3070141,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM7 monocytes,GSM3070141,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070141,GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq,GSM3070141,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM7 monocytes,GSM3070141,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070141,GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq,GSM3070141,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM7 monocytes,GSM3070141,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070141,GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq,GSM3070141,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM6 unenriched,GSM3070140,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070140,GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq,GSM3070140,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM6 unenriched,GSM3070140,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070140,GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq,GSM3070140,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM6 unenriched,GSM3070140,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070140,GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq,GSM3070140,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM6 unenriched,GSM3070140,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070140,GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq,GSM3070140,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM5 unenriched,GSM3070138,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070138,GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq,GSM3070138,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM5 unenriched,GSM3070138,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070138,GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq,GSM3070138,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM5 unenriched,GSM3070138,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070138,GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq,GSM3070138,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM5 unenriched,GSM3070138,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070138,GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq,GSM3070138,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM5 hspcs,GSM3070136,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070136,GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq,GSM3070136,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM5 hspcs,GSM3070136,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070136,GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq,GSM3070136,,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,,SRP136633,,,WKM5_hspcs_L002_R1_001.fastq.gz WKM5_hspcs_L002_R2_001.fastq.gz,fastq fastq,5921476240.0,39257421.0,GSM3070136 r2,0:75.41 1:75.43,A:1748991850;C:876000140;G:1055863619;T:2239402733;N:1217898,75,75,,,1748991850,876000140,1055863619,2239402733,1217898,SRX3856798,SRS3100390,SRA675960,GEO,Hubrecht Institute,2,0.08014,0.61413,0.04634,0.14581,0.98654,0.8717,0.51292,0.50066,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System 47911,SRR6908703,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.,,pubmed:31585086,,WKM5 hspcs,GSM3070136,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070136,GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq,GSM3070136,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM5 hspcs,GSM3070136,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070136,GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq,GSM3070136,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM4 unenriched,GSM3070135,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070135,GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq,GSM3070135,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM4 unenriched,GSM3070135,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070135,GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq,GSM3070135,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM4 unenriched,GSM3070135,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070135,GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq,GSM3070135,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM4 unenriched,GSM3070135,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070135,GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq,GSM3070135,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM3 unenriched,GSM3070133,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070133,GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq,GSM3070133,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM3 unenriched,GSM3070133,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070133,GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq,GSM3070133,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM3 unenriched,GSM3070133,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070133,GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq,GSM3070133,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM3 unenriched,GSM3070133,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070133,GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq,GSM3070133,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM2 unenriched,GSM3070130,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070130,GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq,GSM3070130,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM2 unenriched,GSM3070130,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070130,GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq,GSM3070130,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM2 unenriched,GSM3070130,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070130,GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq,GSM3070130,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM2 unenriched,GSM3070130,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070130,GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq,GSM3070130,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM1 unenriched and eosinphils,GSM3070127,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070127,GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq,GSM3070127,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM1 unenriched and eosinphils,GSM3070127,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070127,GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq,GSM3070127,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM1 unenriched and eosinphils,GSM3070127,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070127,GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq,GSM3070127,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM1 unenriched and eosinphils,GSM3070127,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070127,GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq,GSM3070127,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM10 unenriched,GSM3070126,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070126,GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq,GSM3070126,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM10 unenriched,GSM3070126,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070126,GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq,GSM3070126,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM10 unenriched,GSM3070126,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070126,GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq,GSM3070126,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM10 unenriched,GSM3070126,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070126,GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq,GSM3070126,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM10 hspcs,GSM3070124,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070124,GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq,GSM3070124,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM10 hspcs,GSM3070124,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070124,GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq,GSM3070124,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM10 hspcs,GSM3070124,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070124,GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq,GSM3070124,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,WKM10 hspcs,GSM3070124,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070124,GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq,GSM3070124,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched6,GSM3070123,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070123,GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq,GSM3070123,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched6,GSM3070123,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070123,GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq,GSM3070123,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched6,GSM3070123,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070123,GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq,GSM3070123,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched6,GSM3070123,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070123,GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq,GSM3070123,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched5,GSM3070122,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070122,GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq,GSM3070122,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched5,GSM3070122,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070122,GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq,GSM3070122,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched5,GSM3070122,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070122,GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq,GSM3070122,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched5,GSM3070122,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070122,GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq,GSM3070122,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched4,GSM3070121,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070121,GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq,GSM3070121,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched4,GSM3070121,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070121,GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq,GSM3070121,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched4,GSM3070121,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070121,GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq,GSM3070121,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched4,GSM3070121,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070121,GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq,GSM3070121,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched3,GSM3070120,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070120,GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq,GSM3070120,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched3,GSM3070120,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070120,GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq,GSM3070120,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched3,GSM3070120,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070120,GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq,GSM3070120,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched3,GSM3070120,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070120,GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq,GSM3070120,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched2,GSM3070119,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070119,GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq,GSM3070119,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched2,GSM3070119,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070119,GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq,GSM3070119,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched2,GSM3070119,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070119,GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq,GSM3070119,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched2,GSM3070119,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070119,GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq,GSM3070119,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched1,GSM3070118,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070118,GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq,GSM3070118,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched1,GSM3070118,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070118,GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq,GSM3070118,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched1,GSM3070118,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070118,GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq,GSM3070118,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD2 unenriched1,GSM3070118,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070118,GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq,GSM3070118,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1c unenriched2,GSM3070117,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070117,GSM3070117: TD1c unenriched2; Danio rerio; RNA Seq,GSM3070117,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1c unenriched2,GSM3070117,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070117,GSM3070117: TD1c unenriched2; Danio rerio; RNA Seq,GSM3070117,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1c unenriched2,GSM3070117,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070117,GSM3070117: TD1c unenriched2; Danio rerio; RNA Seq,GSM3070117,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1c unenriched2,GSM3070117,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070117,GSM3070117: TD1c unenriched2; Danio rerio; RNA Seq,GSM3070117,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1c unenriched1,GSM3070116,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070116,GSM3070116: TD1c unenriched1; Danio rerio; RNA Seq,GSM3070116,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1c unenriched1,GSM3070116,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070116,GSM3070116: TD1c unenriched1; Danio rerio; RNA Seq,GSM3070116,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1c unenriched1,GSM3070116,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070116,GSM3070116: TD1c unenriched1; Danio rerio; RNA Seq,GSM3070116,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1c unenriched1,GSM3070116,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1c|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070116,GSM3070116: TD1c unenriched1; Danio rerio; RNA Seq,GSM3070116,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1b unenriched2,GSM3070115,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070115,GSM3070115: TD1b unenriched2; Danio rerio; RNA Seq,GSM3070115,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1b unenriched2,GSM3070115,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070115,GSM3070115: TD1b unenriched2; Danio rerio; RNA Seq,GSM3070115,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1b unenriched2,GSM3070115,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070115,GSM3070115: TD1b unenriched2; Danio rerio; RNA Seq,GSM3070115,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1b unenriched2,GSM3070115,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070115,GSM3070115: TD1b unenriched2; Danio rerio; RNA Seq,GSM3070115,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1b unenriched1,GSM3070114,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070114,GSM3070114: TD1b unenriched1; Danio rerio; RNA Seq,GSM3070114,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1b unenriched1,GSM3070114,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070114,GSM3070114: TD1b unenriched1; Danio rerio; RNA Seq,GSM3070114,,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,,SRP136633,,,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,,,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,,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.,,pubmed:31585086,,TD1b unenriched1,GSM3070114,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070114,GSM3070114: TD1b unenriched1; Danio rerio; RNA Seq,GSM3070114,,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,,SRP136633,,,TD1b_unenriched1_L003_R1_001.fastq.gz TD1b_unenriched1_L003_R2_001.fastq.gz,fastq fastq,1141480052.0,7561497.0,GSM3070114 r3,0:75.46 1:75.50,A:297889459;C:167277504;G:177906961;T:498398944;N:7184,75,75,,,297889459,167277504,177906961,498398944,7184,SRX3856775,SRS3100367,SRA675960,GEO,Hubrecht Institute,2,0.20135,0.89768,0.15828,0.24254,0.99608,0.85987,0.2962,0.55679,76,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System 48000,SRR6908614,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.,,pubmed:31585086,,TD1b unenriched1,GSM3070114,,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,,post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD1b|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070114,GSM3070114: TD1b unenriched1; Danio rerio; RNA Seq,GSM3070114,,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,,SRP136633,,,TD1b_unenriched1_L004_R1_001.fastq.gz TD1b_unenriched1_L004_R2_001.fastq.gz,fastq fastq,1160580768.0,7687763.0,GSM3070114 r4,0:75.46 1:75.50,A:302256817;C:171158314;G:180891374;T:506272528;N:1735,75,75,,,302256817,171158314,180891374,506272528,1735,SRX3856775,SRS3100367,SRA675960,GEO,Hubrecht Institute,2,0.18867,0.89487,0.14967,0.24538,0.99557,0.86269,0.36386,0.54094,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System