rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,,inDrop sequencing of multiple samples 2,GSM2696104,,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,,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.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696104,GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq,GSM2696104,,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:GSM2696104,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run2_R1.fastq.gz,fastq,23315853588.0,382227108.0,GSM2696104 r1,0:61 1:0,A:6573828142;C:5137891481;G:5021324431;T:6582457296;N:352238,61,0,,,6573828142,5137891481,5021324431,6582457296,352238,SRX2989237,SRS2341160,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.83828,,0.08537,,0.83552,,0.56658,,61,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42600,SRR5810683,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,,inDrop sequencing of multiple samples 2,GSM2696104,,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,,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.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696104,GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq,GSM2696104,,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:GSM2696104,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run2_R2.fastq.gz,fastq,3057816864.0,382227108.0,GSM2696104 r2,0:0 1:8,A:743619897;C:720488231;G:1031094190;T:562297818;N:316728,0,8,,,743619897,720488231,1031094190,562297818,316728,SRX2989237,SRS2341160,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42601,SRR5810684,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,,inDrop sequencing of multiple samples 2,GSM2696104,,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,,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.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696104,GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq,GSM2696104,,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:GSM2696104,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run2_R3.fastq.gz,fastq,3057816864.0,382227108.0,GSM2696104 r3,0:8,A:913664473;C:577895371;G:646194239;T:918893384;N:1169397,8,,,,913664473,577895371,646194239,918893384,1169397,SRX2989237,SRS2341160,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42602,SRR5810685,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,,inDrop sequencing of multiple samples 2,GSM2696104,,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,,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.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696104,GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq,GSM2696104,,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:GSM2696104,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run2_R4.fastq.gz,fastq,5351179512.0,382227108.0,GSM2696104 r4,0:14,A:1351470715;C:1294400719;G:1379073889;T:1322397488;N:3836701,14,,,,1351470715,1294400719,1379073889,1322397488,3836701,SRX2989237,SRS2341160,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,14,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42603,SRR5810678,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,,inDrop sequencing of multiple samples 1,GSM2696103,,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,,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.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696103,GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq,GSM2696103,,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,,SRP111339,,,inDrop_v3_run1_R1.fastq.gz,fastq,26868371039.0,440465099.0,GSM2696103 r1,0:61 1:0,A:7598044404;C:5948542485;G:5746339343;T:7575168754;N:276053,61,0,,,7598044404,5948542485,5746339343,7575168754,276053,SRX2989236,SRS2341159,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.83437,,0.08222,,0.82658,,0.54569,,61,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42604,SRR5810679,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,,inDrop sequencing of multiple samples 1,GSM2696103,,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,,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.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696103,GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq,GSM2696103,,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,,SRP111339,,,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,,,892841722,781074758,1176856476,672376743,571093,SRX2989236,SRS2341159,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of multiple samples 1,GSM2696103,,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,,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.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696103,GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq,GSM2696103,,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,,SRP111339,,,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,,,,1016854893,682256486,759860179,1063129659,1619575,SRX2989236,SRS2341159,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of multiple samples 1,GSM2696103,,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,,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.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696103,GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq,GSM2696103,,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,,SRP111339,,,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,,,,1513770161,1469643118,1669791951,1509862301,3443855,SRX2989236,SRS2341159,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,14,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2,GSM2696102,,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,,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.,,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,,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,,SRP111339,,,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,,,506372087,413396954,415448050,652683387,28918,SRX2989235,SRS2341158,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.86587,,0.12447,,0.80336,,0.54126,,36,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2,GSM2696102,,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,,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.,,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,,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,,SRP111339,,,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,,,554483675,506568509,721419849,974751566,3789451,SRX2989235,SRS2341158,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.00796,,0.0077,,0.99961,,0.78947,,50,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1,GSM2696101,,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,,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.,,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,,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,,SRP111339,,,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,,,402261661,326108405,319637981,501413963,20726,SRX2989234,SRS2341157,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.84263,,0.11449,,0.79464,,0.57001,,36,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1,GSM2696101,,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,,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.,,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,,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,,SRP111339,,,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,,,432547886,403759182,561234660,751564536,2897536,SRX2989234,SRS2341157,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.00796,,0.00773,,0.99971,,0.82758,,50,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of WT sample animal #2,GSM2696100,,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,,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.,,indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype,GSM2696100,GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq,GSM2696100,,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,,SRP111339,,,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,,,821476951,657776656,665293293,1057448635,46965,SRX2989233,SRS2341156,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.84222,,0.12969,,0.80683,,0.53542,,36,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of WT sample animal #2,GSM2696100,,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,,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.,,indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype,GSM2696100,GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq,GSM2696100,,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,,SRP111339,,,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,,,880464480,827380868,1171423978,1561925150,6086774,SRX2989233,SRS2341156,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.00782,,0.0075,,0.99947,,0.91666,,50,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of WT sample animal #1,GSM2696099,,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,,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.,,indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype,GSM2696099,GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq,GSM2696099,,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,,SRP111339,,,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,,,858288917,693848400,675650809,1085369048,48322,SRX2989232,SRS2341155,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.8771,,0.13918,,0.81115,,0.59004,,36,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,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,,inDrop sequencing of WT sample animal #1,GSM2696099,,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,,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.,,indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype,GSM2696099,GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq,GSM2696099,,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,,SRP111339,,,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,,,914884703,856837987,1192418010,1631240786,6292814,SRX2989232,SRS2341155,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0063,,0.00598,,0.99959,,0.8913,,50,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,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,,,kdrl:GFP+  adult kidney,GSM7091842,,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. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426651,,,FLK-G_Single_Cell_ACTCTAGG.fastq.sorted.fastq.gz,fastq,10648313404.0,80407702.0,GSM7091842 r1,0:132.43,A:3393628100;C:2087372845;G:1953079760;T:3213786135;N:446564,132,,,,3393628100,2087372845,1953079760,3213786135,446564,SRX19635460,SRS17004492,,,"Oncology/Hematology, Boston Children's Hospital",1,0.60891,,0.10525,,0.81903,,0.52577,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Adult,Adult,Kidney,Renal System
74456,SRR23804141,SRX19635459,SRS17004491,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,,,kdrl:mCherry+  adult kidney  rep2,GSM7091841,,source name:kdrl:mCherry transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney,kdrl:mCherry+  adult kidney  rep2,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:mCherry 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,GSM7091841,GSM7091841: kdrl:mCherry+  adult kidney  rep2; Danio rerio; RNA Seq,GSM7091841 r1,GSM7091841,1,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. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426651,,,FLK-R_Single_Cell_CTAGTCGA.fastq.sorted.fastq.gz,fastq,13922952441.0,105098464.0,GSM7091841 r1,0:132.48,A:4341235438;C:2807868369;G:2579519980;T:4193742000;N:586654,132,,,,4341235438,2807868369,2579519980,4193742000,586654,SRX19635459,SRS17004491,,,"Oncology/Hematology, Boston Children's Hospital",1,0.64512,,0.12315,,0.81712,,0.52922,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Adult,Adult,Kidney,Renal System
74457,SRR23804142,SRX19635458,SRS17004490,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,,,kdrl:mCherry+  adult kidney  rep1,GSM7091840,,source name:kdrl:mCherry transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney,kdrl:mCherry+  adult kidney  rep1,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:mCherry 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,GSM7091840,GSM7091840: kdrl:mCherry+  adult kidney  rep1; Danio rerio; RNA Seq,GSM7091840 r1,GSM7091840,1,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. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426651,,,KLR_Single_Cell_ATTAGACG.fastq.sorted.fastq.gz,fastq,8774502682.0,64692571.0,GSM7091840 r1,0:135.63,A:2791773089;C:1725088037;G:1633088372;T:2624197073;N:356111,135,,,,2791773089,1725088037,1633088372,2624197073,356111,SRX19635458,SRS17004490,,,"Oncology/Hematology, Boston Children's Hospital",1,0.66981,,0.10372,,0.81357,,0.5394,,38,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Adult,Adult,Kidney,Renal System