{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Adult\" and technology = \"indrops\"", "rows": [[42599, "SRR5810682", "SRX2989237", "SRS2341160", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 2", "GSM2696104", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. 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Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 2", "GSM2696104", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696104", "GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq", "GSM2696104", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. 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Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 2", "GSM2696104", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696104", "GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq", "GSM2696104", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. 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Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 2", "GSM2696104", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696104", "GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq", "GSM2696104", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. 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Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 1", "GSM2696103", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696103", "GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq", "GSM2696103", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. 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Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 1", "GSM2696103", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696103", "GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq", "GSM2696103", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run1_R2.fastq.gz", "fastq", 3523720792.0, 440465099.0, "GSM2696103 r2", "0:0 1:8", "A:892841722;C:781074758;G:1176856476;T:672376743;N:571093", 0, 8, null, null, 892841722, 781074758, 1176856476, 672376743, 571093, "SRX2989236", "SRS2341159", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42605, "SRR5810680", "SRX2989236", "SRS2341159", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 1", "GSM2696103", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696103", "GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq", "GSM2696103", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run1_R3.fastq.gz", "fastq", 3523720792.0, 440465099.0, "GSM2696103 r3", "0:8", "A:1016854893;C:682256486;G:759860179;T:1063129659;N:1619575", 8, null, null, null, 1016854893, 682256486, 759860179, 1063129659, 1619575, "SRX2989236", "SRS2341159", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42606, "SRR5810681", "SRX2989236", "SRS2341159", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 1", "GSM2696103", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696103", "GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq", "GSM2696103", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run1_R4.fastq.gz", "fastq", 6166511386.0, 440465099.0, "GSM2696103 r4", "0:14", "A:1513770161;C:1469643118;G:1669791951;T:1509862301;N:3443855", 14, null, null, null, 1513770161, 1469643118, 1669791951, 1509862301, 3443855, "SRX2989236", "SRS2341159", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 14, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42607, "SRR5810676", "SRX2989235", "SRS2341158", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2", "GSM2696102", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "GSM2696102", "GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq", "GSM2696102", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "PRKDC2_R1.fastq.gz", "fastq", 1987929396.0, 55220261.0, "GSM2696102 r1", "0:36 1:0", "A:506372087;C:413396954;G:415448050;T:652683387;N:28918", 36, 0, null, null, 506372087, 413396954, 415448050, 652683387, 28918, "SRX2989235", "SRS2341158", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.86587, null, 0.12447, null, 0.80336, null, 0.54126, null, 36, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42608, "SRR5810677", "SRX2989235", "SRS2341158", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2", "GSM2696102", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "GSM2696102", "GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq", "GSM2696102", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "PRKDC2_R2.fastq.gz", "fastq", 2761013050.0, 55220261.0, "GSM2696102 r2", "0:0 1:50", "A:554483675;C:506568509;G:721419849;T:974751566;N:3789451", 0, 50, null, null, 554483675, 506568509, 721419849, 974751566, 3789451, "SRX2989235", "SRS2341158", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.00796, null, 0.0077, null, 0.99961, null, 0.78947, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42609, "SRR5810674", "SRX2989234", "SRS2341157", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1", "GSM2696101", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "GSM2696101", "GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq", "GSM2696101", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "PRKDC1_R1.fastq.gz", "fastq", 1549442736.0, 43040076.0, "GSM2696101 r1", "0:36 1:0", "A:402261661;C:326108405;G:319637981;T:501413963;N:20726", 36, 0, null, null, 402261661, 326108405, 319637981, 501413963, 20726, "SRX2989234", "SRS2341157", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.84263, null, 0.11449, null, 0.79464, null, 0.57001, null, 36, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42610, "SRR5810675", "SRX2989234", "SRS2341157", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1", "GSM2696101", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "GSM2696101", "GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq", "GSM2696101", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "PRKDC1_R2.fastq.gz", "fastq", 2152003800.0, 43040076.0, "GSM2696101 r2", "0:0 1:50", "A:432547886;C:403759182;G:561234660;T:751564536;N:2897536", 0, 50, null, null, 432547886, 403759182, 561234660, 751564536, 2897536, "SRX2989234", "SRS2341157", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.00796, null, 0.00773, null, 0.99971, null, 0.82758, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42611, "SRR5810672", "SRX2989233", "SRS2341156", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of WT sample animal #2", "GSM2696100", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "inDrop sequencing of WT sample animal #2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "GSM2696100", "GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq", "GSM2696100", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "WT2_R1.fastq.gz", "fastq", 3202042500.0, 88945625.0, "GSM2696100 r1", "0:36 1:0", "A:821476951;C:657776656;G:665293293;T:1057448635;N:46965", 36, 0, null, null, 821476951, 657776656, 665293293, 1057448635, 46965, "SRX2989233", "SRS2341156", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.84222, null, 0.12969, null, 0.80683, null, 0.53542, null, 36, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42612, "SRR5810673", "SRX2989233", "SRS2341156", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of WT sample animal #2", "GSM2696100", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "inDrop sequencing of WT sample animal #2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "GSM2696100", "GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq", "GSM2696100", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "WT2_R2.fastq.gz", "fastq", 4447281250.0, 88945625.0, "GSM2696100 r2", "0:0 1:50", "A:880464480;C:827380868;G:1171423978;T:1561925150;N:6086774", 0, 50, null, null, 880464480, 827380868, 1171423978, 1561925150, 6086774, "SRX2989233", "SRS2341156", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.00782, null, 0.0075, null, 0.99947, null, 0.91666, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42613, "SRR5810670", "SRX2989232", "SRS2341155", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of WT sample animal #1", "GSM2696099", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "inDrop sequencing of WT sample animal #1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "GSM2696099", "GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq", "GSM2696099", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "WT1_R1.fastq.gz", "fastq", 3313205496.0, 92033486.0, "GSM2696099 r1", "0:36 1:0", "A:858288917;C:693848400;G:675650809;T:1085369048;N:48322", 36, 0, null, null, 858288917, 693848400, 675650809, 1085369048, 48322, "SRX2989232", "SRS2341155", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.8771, null, 0.13918, null, 0.81115, null, 0.59004, null, 36, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42614, "SRR5810671", "SRX2989232", "SRS2341155", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of WT sample animal #1", "GSM2696099", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "inDrop sequencing of WT sample animal #1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly  reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "GSM2696099", "GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq", "GSM2696099", null, "1", "RNA from individual cells were reverse transcribed  barcoded  and unique transcripts are imprinted with UMI  all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions  and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents.  This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "WT1_R2.fastq.gz", "fastq", 4601674300.0, 92033486.0, "GSM2696099 r2", "0:0 1:50", "A:914884703;C:856837987;G:1192418010;T:1631240786;N:6292814", 0, 50, null, null, 914884703, 856837987, 1192418010, 1631240786, 6292814, "SRX2989232", "SRS2341155", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0063, null, 0.00598, null, 0.99959, null, 0.8913, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [59301, "SRR11851897", "SRX8402007", "SRS6714764", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b ko 3", "GSM4568915", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "scRNA seq gata2b ko 3", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "GSM4568915", "GSM4568915: scRNA seq gata2b ko 3; Danio rerio; RNA Seq", "GSM4568915", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568915", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "KO3_Single_Cell_GAGACGGA.fastq.sorted.fastq.gz", "fastq", 3768784245.0, 63353331.0, "GSM4568915 r1", "0:59.49", "A:1049235928;C:815061845;G:790664763;T:1113812557;N:9152", 59, null, null, null, 1049235928, 815061845, 790664763, 1113812557, 9152, "SRX8402007", "SRS6714764", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.9009, null, 0.07395, null, 0.83524, null, 0.54215, null, 60, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59302, "SRR11851896", "SRX8402006", "SRS6714763", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b ko 2", "GSM4568914", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "scRNA seq gata2b ko 2", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "GSM4568914", "GSM4568914: scRNA seq gata2b ko 2; Danio rerio; RNA Seq", "GSM4568914", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568914", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "KO2_Single_Cell_TTACCTCC.fastq.sorted.fastq.gz", "fastq", 5788926123.0, 96793878.0, "GSM4568914 r1", "0:59.81", "A:1591846184;C:1284226924;G:1217400432;T:1695437315;N:15268", 59, null, null, null, 1591846184, 1284226924, 1217400432, 1695437315, 15268, "SRX8402006", "SRS6714763", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.90311, null, 0.0768, null, 0.82227, null, 0.56806, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59303, "SRR11851895", "SRX8402005", "SRS6714762", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b ko 1", "GSM4568913", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "scRNA seq gata2b ko 1", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "GSM4568913", "GSM4568913: scRNA seq gata2b ko 1; Danio rerio; RNA Seq", "GSM4568913", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568913", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "KO1_Single_Cell_TAAGGCTC.fastq.sorted.fastq.gz", "fastq", 4485434923.0, 75329131.0, "GSM4568913 r1", "0:59.54", "A:1245571394;C:1005814804;G:944318855;T:1289711080;N:18790", 59, null, null, null, 1245571394, 1005814804, 944318855, 1289711080, 18790, "SRX8402005", "SRS6714762", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.89937, null, 0.06305, null, 0.83879, null, 0.54954, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59304, "SRR11851894", "SRX8402004", "SRS6714761", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b het 3", "GSM4568912", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "scRNA seq gata2b het 3", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "GSM4568912", "GSM4568912: scRNA seq gata2b het 3; Danio rerio; RNA Seq", "GSM4568912", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568912", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "HET3_Single_Cell_CCTTTACT.fastq.sorted.fastq.gz", "fastq", 3696586389.0, 62109708.0, "GSM4568912 r1", "0:59.52", "A:1054965741;C:827475497;G:744430159;T:1069699165;N:15827", 59, null, null, null, 1054965741, 827475497, 744430159, 1069699165, 15827, "SRX8402004", "SRS6714761", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.89246, null, 0.06392, null, 0.83934, null, 0.56422, null, 58, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59305, "SRR11851893", "SRX8402003", "SRS6714760", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b het 2", "GSM4568911", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "scRNA seq gata2b het 2", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "GSM4568911", "GSM4568911: scRNA seq gata2b het 2; Danio rerio; RNA Seq", "GSM4568911", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568911", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "HET2_Single_Cell_CAGTTATG.fastq.sorted.fastq.gz", "fastq", 5357974983.0, 89558550.0, "GSM4568911 r1", "0:59.83", "A:1490260317;C:1191725100;G:1122517464;T:1553457613;N:14489", 59, null, null, null, 1490260317, 1191725100, 1122517464, 1553457613, 14489, "SRX8402003", "SRS6714760", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.90302, null, 0.07865, null, 0.82603, null, 0.57406, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59306, "SRR11851892", "SRX8402002", "SRS6714759", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b het 1", "GSM4568910", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "scRNA seq gata2b het 1", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "GSM4568910", "GSM4568910: scRNA seq gata2b het 1; Danio rerio; RNA Seq", "GSM4568910", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568910", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "HET1_Single_Cell_ATAGCCTT.fastq.sorted.fastq.gz", "fastq", 4701831804.0, 78923769.0, "GSM4568910 r1", "0:59.57", "A:1307674780;C:1043797904;G:1001646002;T:1348693620;N:19498", 59, null, null, null, 1307674780, 1043797904, 1001646002, 1348693620, 19498, "SRX8402002", "SRS6714759", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.90603, null, 0.07667, null, 0.82704, null, 0.57543, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59307, "SRR11851891", "SRX8402001", "SRS6714758", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq wildtype 3", "GSM4568909", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:wildtype", "scRNA seq wildtype 3", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:wildtype", "GSM4568909", "GSM4568909: scRNA seq wildtype 3; Danio rerio; RNA Seq", "GSM4568909", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568909", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "WT3_Single_Cell_AGAAAGCT.fastq.sorted.fastq.gz", "fastq", 3348785686.0, 56255768.0, "GSM4568909 r1", "0:59.53", "A:955572407;C:728586737;G:678902164;T:985710022;N:14356", 59, null, null, null, 955572407, 728586737, 678902164, 985710022, 14356, "SRX8402001", "SRS6714758", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.88271, null, 0.06967, null, 0.8284, null, 0.54728, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59308, "SRR11851890", "SRX8402000", "SRS6714757", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq wildtype 2", "GSM4568908", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:wildtype", "scRNA seq wildtype 2", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:wildtype", "GSM4568908", "GSM4568908: scRNA seq wildtype 2; Danio rerio; RNA Seq", "GSM4568908", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568908", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "WT2_Single_Cell_TCGCATAA.fastq.sorted.fastq.gz", "fastq", 3812899254.0, 63738225.0, "GSM4568908 r1", "0:59.82", "A:1040969741;C:863166087;G:810647668;T:1098105772;N:9986", 59, null, null, null, 1040969741, 863166087, 810647668, 1098105772, 9986, "SRX8402000", "SRS6714757", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.91023, null, 0.06938, null, 0.83238, null, 0.54799, null, 59, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59309, "SRR11851889", "SRX8401999", "SRS6714756", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias  atypical infections  and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 /  mice  the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here  we generated a zebrafish mutant of gata2b  which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses  we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors  gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype  gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper  n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types  comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq wildtype 1", "GSM4568907", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:wildtype", "scRNA seq wildtype 1", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system  with 75 cycle kit  with pair end reads Read1: 61 cycles  Read2: 14 cycles  Index 1: 8 cycles  Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al.  2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice  every 45 60 min for processing.", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:wildtype", "GSM4568907", "GSM4568907: scRNA seq wildtype 1; Danio rerio; RNA Seq", "GSM4568907", null, "1", "post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion  every 45 60min  were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core.  https://github.com/indrops/indrops", "GEO Accession:GSM4568907", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options:  appendBCtoName", "WT1_Single_Cell_CTTAATAG.fastq.sorted.fastq.gz", "fastq", 3675748091.0, 61731984.0, "GSM4568907 r1", "0:59.54", "A:1040800033;C:822608649;G:765542043;T:1046781383;N:15983", 59, null, null, null, 1040800033, 822608649, 765542043, 1046781383, 15983, "SRX8401999", "SRS6714756", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.8978, null, 0.05341, null, 0.84167, null, 0.59389, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [74455, "SRR23804140", "SRX19635460", "SRS17004492", "SRP426651", "PRJNA943248", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]", "GSE227115", "Transcriptome Analysis", "We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected  homogenized  filtered  and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "kdrl:GFP+  adult kidney", "GSM7091842", null, "source name:kdrl:GFP transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney", "kdrl:GFP+  adult kidney", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "kdrl:GFP transgenic zebrafish adult kidney wild type", "No treatments", "Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer.  Adult kidneys were dissected then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.", "developmental stage:adult|genotype:wild type|tissue:kidney", "GSM7091842", "GSM7091842: kdrl:GFP+  adult kidney; Danio rerio; RNA Seq", "GSM7091842 r1", "GSM7091842", "1", "Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. 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