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
42627,SRR5810931,SRX2989483,SRS2341405,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D12,GSM2696350,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696350,GSM2696350: Runx123 GFP.P1.D12; Danio rerio; RNA Seq,GSM2696350,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696350,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D12.bam,bam,80381537.0,1070203.0,GSM2696350 r1,0:37.55 1:37.56,A:21289298;C:18976641;G:18646654;T:21447816;N:21128,37,37,,,21289298,18976641,18646654,21447816,21128,SRX2989483,SRS2341405,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.87699,0.87627,0.08393,0.08323,0.94385,0.94432,0.47664,0.47751,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42628,SRR5810930,SRX2989482,SRS2341406,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D11,GSM2696349,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696349,GSM2696349: Runx123 GFP.P1.D11; Danio rerio; RNA Seq,GSM2696349,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696349,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D11.bam,bam,110475987.0,1471507.0,GSM2696349 r1,0:37.54 1:37.54,A:28733566;C:26637046;G:26164058;T:28909002;N:32315,37,37,,,28733566,26637046,26164058,28909002,32315,SRX2989482,SRS2341406,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.86384,0.86659,0.0745,0.07357,0.95026,0.95069,0.43802,0.44268,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42629,SRR5810929,SRX2989481,SRS2341404,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D10,GSM2696348,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D10,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696348,GSM2696348: Runx123 GFP.P1.D10; Danio rerio; RNA Seq,GSM2696348,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696348,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D10.bam,bam,64029006.0,852803.0,GSM2696348 r1,0:37.54 1:37.54,A:16672853;C:15398688;G:15154223;T:16784255;N:18987,37,37,,,16672853,15398688,15154223,16784255,18987,SRX2989481,SRS2341404,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.86959,0.86933,0.07603,0.07599,0.95371,0.95426,0.42353,0.46566,36,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42630,SRR5810928,SRX2989480,SRS2341403,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D09,GSM2696347,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D09,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696347,GSM2696347: Runx123 GFP.P1.D09; Danio rerio; RNA Seq,GSM2696347,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696347,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D09.bam,bam,47224779.0,627954.0,GSM2696347 r1,0:37.60 1:37.60,A:13328909;C:10314542;G:10086676;T:13486101;N:8551,37,37,,,13328909,10314542,10086676,13486101,8551,SRX2989480,SRS2341403,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91771,0.91801,0.2846,0.28357,0.98382,0.98441,0.51864,0.48968,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42631,SRR5810927,SRX2989479,SRS2341402,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D07,GSM2696346,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D07,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696346,GSM2696346: Runx123 GFP.P1.D07; Danio rerio; RNA Seq,GSM2696346,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696346,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D07.bam,bam,95937754.0,1276149.0,GSM2696346 r1,0:37.59 1:37.59,A:26235960;C:21834939;G:21328613;T:26519033;N:19209,37,37,,,26235960,21834939,21328613,26519033,19209,SRX2989479,SRS2341402,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91901,0.9191,0.21301,0.21363,0.97569,0.97636,0.50099,0.48645,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42632,SRR5810926,SRX2989478,SRS2341401,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D05,GSM2696345,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696345,GSM2696345: Runx123 GFP.P1.D05; Danio rerio; RNA Seq,GSM2696345,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696345,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D05.bam,bam,63200305.0,841042.0,GSM2696345 r1,0:37.57 1:37.57,A:16679985;C:14999740;G:14596412;T:16911795;N:12373,37,37,,,16679985,14999740,14596412,16911795,12373,SRX2989478,SRS2341401,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92517,0.92801,0.09142,0.09164,0.92423,0.92476,0.49349,0.50932,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42633,SRR5810925,SRX2989477,SRS2341400,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D04,GSM2696344,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696344,GSM2696344: Runx123 GFP.P1.D04; Danio rerio; RNA Seq,GSM2696344,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696344,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D04.bam,bam,116667635.0,1552599.0,GSM2696344 r1,0:37.57 1:37.57,A:30673358;C:27825004;G:27081912;T:31064756;N:22605,37,37,,,30673358,27825004,27081912,31064756,22605,SRX2989477,SRS2341400,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92555,0.92526,0.07819,0.07883,0.90179,0.9026,0.50917,0.4991,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42634,SRR5810924,SRX2989476,SRS2341397,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D03,GSM2696343,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696343,GSM2696343: Runx123 GFP.P1.D03; Danio rerio; RNA Seq,GSM2696343,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696343,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D03.bam,bam,17871672.0,237645.0,GSM2696343 r1,0:37.60 1:37.60,A:5018355;C:3926970;G:3841973;T:5081075;N:3299,37,37,,,5018355,3926970,3841973,5081075,3299,SRX2989476,SRS2341397,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91431,0.91617,0.27987,0.27943,0.9811,0.98177,0.46989,0.47788,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42635,SRR5810923,SRX2989475,SRS2341399,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D02,GSM2696342,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D02,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696342,GSM2696342: Runx123 GFP.P1.D02; Danio rerio; RNA Seq,GSM2696342,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696342,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D02.bam,bam,5910004.0,78559.0,GSM2696342 r1,0:37.62 1:37.61,A:1696500;C:1262727;G:1225976;T:1723800;N:1001,37,37,,,1696500,1262727,1225976,1723800,1001,SRX2989475,SRS2341399,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90278,0.90711,0.30589,0.30762,0.98514,0.98537,0.53428,0.50422,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42636,SRR5810922,SRX2989474,SRS2341396,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.D01,GSM2696341,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.D01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696341,GSM2696341: Runx123 GFP.P1.D01; Danio rerio; RNA Seq,GSM2696341,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696341,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.D01.bam,bam,80127770.0,1066187.0,GSM2696341 r1,0:37.58 1:37.58,A:21326419;C:18808312;G:18299957;T:21677439;N:15643,37,37,,,21326419,18808312,18299957,21677439,15643,SRX2989474,SRS2341396,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92107,0.92092,0.13232,0.13185,0.94757,0.94882,0.51086,0.51778,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42637,SRR5810921,SRX2989473,SRS2341398,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C12,GSM2696340,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696340,GSM2696340: Runx123 GFP.P1.C12; Danio rerio; RNA Seq,GSM2696340,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696340,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C12.bam,bam,111631740.0,1485455.0,GSM2696340 r1,0:37.57 1:37.58,A:29772997;C:26221160;G:25531927;T:30084216;N:21440,37,37,,,29772997,26221160,25531927,30084216,21440,SRX2989473,SRS2341398,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92285,0.92236,0.08777,0.08728,0.90433,0.90526,0.50931,0.51179,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42638,SRR5810920,SRX2989472,SRS2341395,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C11,GSM2696339,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696339,GSM2696339: Runx123 GFP.P1.C11; Danio rerio; RNA Seq,GSM2696339,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696339,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C11.bam,bam,88068314.0,1172143.0,GSM2696339 r1,0:37.57 1:37.57,A:23113672;C:21054221;G:20500170;T:23381662;N:18589,37,37,,,23113672,21054221,20500170,23381662,18589,SRX2989472,SRS2341395,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91721,0.91633,0.05241,0.05228,0.95501,0.95491,0.52219,0.51522,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42639,SRR5810919,SRX2989471,SRS2341394,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C10,GSM2696338,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C10,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696338,GSM2696338: Runx123 GFP.P1.C10; Danio rerio; RNA Seq,GSM2696338,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696338,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C10.bam,bam,38361252.0,510997.0,GSM2696338 r1,0:37.54 1:37.54,A:9899029;C:9318645;G:9172551;T:9959598;N:11429,37,37,,,9899029,9318645,9172551,9959598,11429,SRX2989471,SRS2341394,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.86389,0.86228,0.05704,0.05555,0.97699,0.97731,0.44695,0.44501,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42640,SRR5810918,SRX2989470,SRS2341392,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C09,GSM2696337,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C09,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696337,GSM2696337: Runx123 GFP.P1.C09; Danio rerio; RNA Seq,GSM2696337,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696337,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C09.bam,bam,68798519.0,914900.0,GSM2696337 r1,0:37.60 1:37.60,A:19292535;C:15146911;G:14826092;T:19520460;N:12521,37,37,,,19292535,15146911,14826092,19520460,12521,SRX2989470,SRS2341392,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91662,0.91722,0.28132,0.28066,0.98334,0.9834,0.45843,0.45913,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42641,SRR5810917,SRX2989469,SRS2341393,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C07,GSM2696336,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C07,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696336,GSM2696336: Runx123 GFP.P1.C07; Danio rerio; RNA Seq,GSM2696336,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696336,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C07.bam,bam,132672266.0,1765198.0,GSM2696336 r1,0:37.58 1:37.58,A:35515458;C:30979554;G:30191689;T:35959966;N:25599,37,37,,,35515458,30979554,30191689,35959966,25599,SRX2989469,SRS2341393,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9221,0.92377,0.13303,0.13251,0.94659,0.94744,0.48291,0.484,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42642,SRR5810916,SRX2989468,SRS2341391,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C06,GSM2696335,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C06,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696335,GSM2696335: Runx123 GFP.P1.C06; Danio rerio; RNA Seq,GSM2696335,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696335,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C06.bam,bam,84779265.0,1127489.0,GSM2696335 r1,0:37.59 1:37.60,A:23538252;C:18907613;G:18492124;T:23826770;N:14506,37,37,,,23538252,18907613,18492124,23826770,14506,SRX2989468,SRS2341391,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91446,0.91456,0.26601,0.26665,0.98494,0.98514,0.51766,0.52126,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42643,SRR5810915,SRX2989467,SRS2341390,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C05,GSM2696334,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696334,GSM2696334: Runx123 GFP.P1.C05; Danio rerio; RNA Seq,GSM2696334,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696334,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C05.bam,bam,80373171.0,1069341.0,GSM2696334 r1,0:37.58 1:37.58,A:21548703;C:18732066;G:18228538;T:21847949;N:15915,37,37,,,21548703,18732066,18228538,21847949,15915,SRX2989467,SRS2341390,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92431,0.92384,0.14745,0.14636,0.94933,0.94929,0.49522,0.48798,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42644,SRR5810914,SRX2989466,SRS2341388,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C04,GSM2696333,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696333,GSM2696333: Runx123 GFP.P1.C04; Danio rerio; RNA Seq,GSM2696333,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696333,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C04.bam,bam,124894345.0,1662046.0,GSM2696333 r1,0:37.57 1:37.57,A:32951583;C:29685078;G:28861190;T:33372638;N:23856,37,37,,,32951583,29685078,28861190,33372638,23856,SRX2989466,SRS2341388,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92688,0.92681,0.08279,0.08229,0.92064,0.92155,0.52192,0.52012,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42645,SRR5810913,SRX2989465,SRS2341387,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C03,GSM2696332,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696332,GSM2696332: Runx123 GFP.P1.C03; Danio rerio; RNA Seq,GSM2696332,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696332,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C03.bam,bam,52251566.0,695041.0,GSM2696332 r1,0:37.59 1:37.59,A:14281983;C:11886324;G:11596671;T:14476869;N:9719,37,37,,,14281983,11886324,11596671,14476869,9719,SRX2989465,SRS2341387,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91524,0.9151,0.18959,0.1887,0.96067,0.96077,0.45598,0.49671,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42646,SRR5810912,SRX2989464,SRS2341389,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C02,GSM2696331,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C02,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696331,GSM2696331: Runx123 GFP.P1.C02; Danio rerio; RNA Seq,GSM2696331,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696331,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C02.bam,bam,12001376.0,159695.0,GSM2696331 r1,0:37.58 1:37.58,A:3192413;C:2820081;G:2753190;T:3233261;N:2431,37,37,,,3192413,2820081,2753190,3233261,2431,SRX2989464,SRS2341389,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92637,0.92622,0.10813,0.10815,0.93515,0.93531,0.50246,0.50502,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42647,SRR5810911,SRX2989463,SRS2341386,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.C01,GSM2696330,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.C01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696330,GSM2696330: Runx123 GFP.P1.C01; Danio rerio; RNA Seq,GSM2696330,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696330,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.C01.bam,bam,144381060.0,1921438.0,GSM2696330 r1,0:37.57 1:37.57,A:38239042;C:34184469;G:33246899;T:38682767;N:27883,37,37,,,38239042,34184469,33246899,38682767,27883,SRX2989463,SRS2341386,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92638,0.92732,0.06569,0.06584,0.92301,0.92358,0.50911,0.4995,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42648,SRR5810910,SRX2989462,SRS2341385,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.B12,GSM2696329,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.B12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696329,GSM2696329: Runx123 GFP.P1.B12; Danio rerio; RNA Seq,GSM2696329,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696329,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.B12.bam,bam,117198871.0,1559287.0,GSM2696329 r1,0:37.58 1:37.58,A:31816554;C:26929456;G:26203100;T:32227582;N:22179,37,37,,,31816554,26929456,26203100,32227582,22179,SRX2989462,SRS2341385,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9156,0.91553,0.13034,0.1312,0.93785,0.93874,0.51145,0.50275,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42649,SRR5810909,SRX2989461,SRS2341384,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.B10,GSM2696328,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.B10,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696328,GSM2696328: Runx123 GFP.P1.B10; Danio rerio; RNA Seq,GSM2696328,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696328,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.B10.bam,bam,81830143.0,1088700.0,GSM2696328 r1,0:37.58 1:37.58,A:22083784;C:18952625;G:18451060;T:22326965;N:15709,37,37,,,22083784,18952625,18451060,22326965,15709,SRX2989461,SRS2341384,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92296,0.92455,0.13679,0.13773,0.95361,0.95432,0.48069,0.48697,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42650,SRR5810908,SRX2989460,SRS2341383,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.B08,GSM2696327,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.B08,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696327,GSM2696327: Runx123 GFP.P1.B08; Danio rerio; RNA Seq,GSM2696327,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696327,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.B08.bam,bam,142205131.0,1893127.0,GSM2696327 r1,0:37.56 1:37.56,A:37131753;C:34113884;G:33438831;T:37487774;N:32889,37,37,,,37131753,34113884,33438831,37487774,32889,SRX2989460,SRS2341383,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.89693,0.89889,0.10925,0.10945,0.94369,0.94424,0.50241,0.50502,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42651,SRR5810907,SRX2989459,SRS2341382,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.B05,GSM2696326,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.B05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696326,GSM2696326: Runx123 GFP.P1.B05; Danio rerio; RNA Seq,GSM2696326,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696326,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.B05.bam,bam,126983826.0,1690889.0,GSM2696326 r1,0:37.55 1:37.55,A:33026361;C:30589990;G:30037590;T:33298071;N:31814,37,37,,,33026361,30589990,30037590,33298071,31814,SRX2989459,SRS2341382,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.89076,0.89215,0.06876,0.06832,0.94554,0.94681,0.47848,0.46333,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42652,SRR5810906,SRX2989458,SRS2341381,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.B04,GSM2696325,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.B04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696325,GSM2696325: Runx123 GFP.P1.B04; Danio rerio; RNA Seq,GSM2696325,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696325,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.B04.bam,bam,122544174.0,1630177.0,GSM2696325 r1,0:37.59 1:37.59,A:33125816;C:28259989;G:27509174;T:33626259;N:22936,37,37,,,33125816,28259989,27509174,33626259,22936,SRX2989458,SRS2341381,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91867,0.91774,0.16669,0.16691,0.95739,0.95816,0.46968,0.48233,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42653,SRR5810905,SRX2989457,SRS2341380,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.B03,GSM2696324,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.B03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696324,GSM2696324: Runx123 GFP.P1.B03; Danio rerio; RNA Seq,GSM2696324,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696324,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.B03.bam,bam,62836732.0,835736.0,GSM2696324 r1,0:37.59 1:37.59,A:17345816;C:14088789;G:13765145;T:17625439;N:11543,37,37,,,17345816,14088789,13765145,17625439,11543,SRX2989457,SRS2341380,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91135,0.91164,0.22828,0.23,0.95657,0.95799,0.48254,0.48557,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42654,SRR5810904,SRX2989456,SRS2341379,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.B02,GSM2696323,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.B02,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696323,GSM2696323: Runx123 GFP.P1.B02; Danio rerio; RNA Seq,GSM2696323,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696323,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.B02.bam,bam,55579726.0,739325.0,GSM2696323 r1,0:37.59 1:37.59,A:15158695;C:12732111;G:12337350;T:15341128;N:10442,37,37,,,15158695,12732111,12337350,15341128,10442,SRX2989456,SRS2341379,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9206,0.92564,0.12141,0.12123,0.932,0.93261,0.52491,0.53084,36,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42655,SRR5810903,SRX2989455,SRS2341378,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.B01,GSM2696322,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.B01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696322,GSM2696322: Runx123 GFP.P1.B01; Danio rerio; RNA Seq,GSM2696322,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696322,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.B01.bam,bam,97175306.0,1292997.0,GSM2696322 r1,0:37.58 1:37.58,A:25961006;C:22751707;G:22103012;T:26340740;N:18841,37,37,,,25961006,22751707,22103012,26340740,18841,SRX2989455,SRS2341378,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91993,0.92006,0.1164,0.11549,0.94077,0.94194,0.52856,0.52534,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42656,SRR5810902,SRX2989454,SRS2341376,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A11,GSM2696321,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696321,GSM2696321: Runx123 GFP.P1.A11; Danio rerio; RNA Seq,GSM2696321,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696321,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A11.bam,bam,55671938.0,740250.0,GSM2696321 r1,0:37.60 1:37.60,A:15655840;C:12190990;G:11931748;T:15883734;N:9626,37,37,,,15655840,12190990,11931748,15883734,9626,SRX2989454,SRS2341376,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90289,0.90262,0.32668,0.32572,0.97074,0.97086,0.5031,0.51683,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42657,SRR5810901,SRX2989453,SRS2341377,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A09,GSM2696320,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A09,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696320,GSM2696320: Runx123 GFP.P1.A09; Danio rerio; RNA Seq,GSM2696320,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696320,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A09.bam,bam,179417367.0,2387224.0,GSM2696320 r1,0:37.58 1:37.58,A:48292938;C:41636027;G:40587884;T:48866235;N:34283,37,37,,,48292938,41636027,40587884,48866235,34283,SRX2989453,SRS2341377,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92302,0.92326,0.13644,0.13752,0.94779,0.94862,0.48378,0.49265,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42658,SRR5810900,SRX2989452,SRS2341375,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A08,GSM2696319,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A08,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696319,GSM2696319: Runx123 GFP.P1.A08; Danio rerio; RNA Seq,GSM2696319,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696319,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A08.bam,bam,159126189.0,2117119.0,GSM2696319 r1,0:37.58 1:37.58,A:43149278;C:36645757;G:35730147;T:43570177;N:30830,37,37,,,43149278,36645757,35730147,43570177,30830,SRX2989452,SRS2341375,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91867,0.91766,0.14618,0.14712,0.96019,0.96187,0.48834,0.4962,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42659,SRR5810899,SRX2989451,SRS2341374,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A07,GSM2696318,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A07,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696318,GSM2696318: Runx123 GFP.P1.A07; Danio rerio; RNA Seq,GSM2696318,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696318,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A07.bam,bam,58771551.0,781510.0,GSM2696318 r1,0:37.60 1:37.60,A:16473933;C:12912665;G:12629036;T:16745570;N:10347,37,37,,,16473933,12912665,12629036,16745570,10347,SRX2989451,SRS2341374,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90899,0.90998,0.27862,0.27924,0.98504,0.98608,0.45606,0.46747,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42660,SRR5810898,SRX2989450,SRS2341373,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A06,GSM2696317,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A06,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696317,GSM2696317: Runx123 GFP.P1.A06; Danio rerio; RNA Seq,GSM2696317,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696317,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A06.bam,bam,140233110.0,1865323.0,GSM2696317 r1,0:37.59 1:37.59,A:38560492;C:31737880;G:30971443;T:38937194;N:26101,37,37,,,38560492,31737880,30971443,38937194,26101,SRX2989450,SRS2341373,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91848,0.91824,0.23265,0.23216,0.97262,0.9726,0.48014,0.48002,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42661,SRR5810897,SRX2989449,SRS2341372,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A05,GSM2696316,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696316,GSM2696316: Runx123 GFP.P1.A05; Danio rerio; RNA Seq,GSM2696316,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696316,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A05.bam,bam,124170196.0,1651790.0,GSM2696316 r1,0:37.59 1:37.59,A:34062267;C:28219948;G:27555733;T:34308702;N:23546,37,37,,,34062267,28219948,27555733,34308702,23546,SRX2989449,SRS2341372,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9207,0.9201,0.17897,0.17898,0.95455,0.9553,0.49553,0.49608,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42662,SRR5810896,SRX2989448,SRS2341371,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A04,GSM2696315,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696315,GSM2696315: Runx123 GFP.P1.A04; Danio rerio; RNA Seq,GSM2696315,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696315,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A04.bam,bam,150251742.0,1999217.0,GSM2696315 r1,0:37.58 1:37.58,A:40047183;C:35282116;G:34306907;T:40586886;N:28650,37,37,,,40047183,35282116,34306907,40586886,28650,SRX2989448,SRS2341371,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92398,0.92406,0.13217,0.1313,0.94414,0.9447,0.50222,0.50658,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42663,SRR5810895,SRX2989447,SRS2341369,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A03,GSM2696314,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696314,GSM2696314: Runx123 GFP.P1.A03; Danio rerio; RNA Seq,GSM2696314,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696314,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A03.bam,bam,102838133.0,1368212.0,GSM2696314 r1,0:37.58 1:37.58,A:27916613;C:23679845;G:23064232;T:28156982;N:20461,37,37,,,27916613,23679845,23064232,28156982,20461,SRX2989447,SRS2341369,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92121,0.92192,0.12738,0.12845,0.94838,0.94909,0.48807,0.49988,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42664,SRR5810894,SRX2989446,SRS2341370,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A02,GSM2696313,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A02,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696313,GSM2696313: Runx123 GFP.P1.A02; Danio rerio; RNA Seq,GSM2696313,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696313,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A02.bam,bam,37280197.0,495818.0,GSM2696313 r1,0:37.59 1:37.60,A:10319799;C:8371049;G:8123905;T:10458151;N:7293,37,37,,,10319799,8371049,8123905,10458151,7293,SRX2989446,SRS2341370,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.913,0.91779,0.17824,0.17822,0.96495,0.96611,0.51175,0.51518,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42665,SRR5810893,SRX2989445,SRS2341368,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,Runx123 GFP.P1.A01,GSM2696312,,source name:whole kidney marrow|tissue:kidney marrow,Runx123 GFP.P1.A01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696312,GSM2696312: Runx123 GFP.P1.A01; Danio rerio; RNA Seq,GSM2696312,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696312,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,Runx123_GFP.P1.A01.bam,bam,75636367.0,1006419.0,GSM2696312 r1,0:37.58 1:37.58,A:20057115;C:17816438;G:17336922;T:20410910;N:14982,37,37,,,20057115,17816438,17336922,20410910,14982,SRX2989445,SRS2341368,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92197,0.92171,0.13753,0.13713,0.94767,0.94823,0.52196,0.51719,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42666,SRR5810892,SRX2989444,SRS2341366,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D12,GSM2696311,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696311,GSM2696311: rag2 GFP.P2.D12; Danio rerio; RNA Seq,GSM2696311,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696311,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D12.bam,bam,18336287.0,243806.0,GSM2696311 r1,0:37.61 1:37.60,A:5238158;C:3941841;G:3849809;T:5303266;N:3213,37,37,,,5238158,3941841,3849809,5303266,3213,SRX2989444,SRS2341366,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90498,0.90585,0.28323,0.28433,0.98031,0.98086,0.47103,0.45526,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42667,SRR5810891,SRX2989443,SRS2341367,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D11,GSM2696310,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696310,GSM2696310: rag2 GFP.P2.D11; Danio rerio; RNA Seq,GSM2696310,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696310,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D11.bam,bam,105860026.0,1408098.0,GSM2696310 r1,0:37.59 1:37.59,A:29590883;C:23482079;G:22917678;T:29849840;N:19546,37,37,,,29590883,23482079,22917678,29849840,19546,SRX2989443,SRS2341367,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91232,0.91086,0.21168,0.21274,0.97686,0.97761,0.50363,0.49791,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42668,SRR5810890,SRX2989442,SRS2341365,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D10,GSM2696309,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D10,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696309,GSM2696309: rag2 GFP.P2.D10; Danio rerio; RNA Seq,GSM2696309,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696309,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D10.bam,bam,113396448.0,1508550.0,GSM2696309 r1,0:37.58 1:37.59,A:31048855;C:25782613;G:25159308;T:31385416;N:20256,37,37,,,31048855,25782613,25159308,31385416,20256,SRX2989442,SRS2341365,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9238,0.92418,0.17217,0.17365,0.97926,0.97964,0.47951,0.47658,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42669,SRR5810889,SRX2989441,SRS2341363,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D09,GSM2696308,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D09,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696308,GSM2696308: rag2 GFP.P2.D09; Danio rerio; RNA Seq,GSM2696308,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696308,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D09.bam,bam,79322046.0,1054999.0,GSM2696308 r1,0:37.59 1:37.59,A:22150256;C:17580460;G:17121788;T:22454972;N:14570,37,37,,,22150256,17580460,17121788,22454972,14570,SRX2989441,SRS2341363,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91629,0.91611,0.24413,0.24557,0.98319,0.98411,0.45659,0.46601,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42670,SRR5810888,SRX2989440,SRS2341364,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D08,GSM2696307,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D08,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696307,GSM2696307: rag2 GFP.P2.D08; Danio rerio; RNA Seq,GSM2696307,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696307,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D08.bam,bam,97315108.0,1293526.0,GSM2696307 r1,0:37.61 1:37.62,A:28277708;C:20425852;G:20047156;T:28548795;N:15597,37,37,,,28277708,20425852,20047156,28548795,15597,SRX2989440,SRS2341364,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.88795,0.88723,0.3754,0.37563,0.9627,0.96319,0.5016,0.50183,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42671,SRR5810887,SRX2989439,SRS2341362,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D07,GSM2696306,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D07,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696306,GSM2696306: rag2 GFP.P2.D07; Danio rerio; RNA Seq,GSM2696306,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696306,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D07.bam,bam,25814611.0,343345.0,GSM2696306 r1,0:37.59 1:37.59,A:7160379;C:5767559;G:5618492;T:7263400;N:4781,37,37,,,7160379,5767559,5618492,7263400,4781,SRX2989439,SRS2341362,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91094,0.91044,0.23203,0.23267,0.98161,0.982,0.5025,0.4792,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42672,SRR5810886,SRX2989438,SRS2341361,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D06,GSM2696305,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D06,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696305,GSM2696305: rag2 GFP.P2.D06; Danio rerio; RNA Seq,GSM2696305,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696305,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D06.bam,bam,141381372.0,1880842.0,GSM2696305 r1,0:37.58 1:37.58,A:38780204;C:32095151;G:31245396;T:39233572;N:27049,37,37,,,38780204,32095151,31245396,39233572,27049,SRX2989438,SRS2341361,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91983,0.91897,0.15478,0.15471,0.9666,0.96773,0.47909,0.4824,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42673,SRR5810885,SRX2989437,SRS2341360,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D05,GSM2696304,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696304,GSM2696304: rag2 GFP.P2.D05; Danio rerio; RNA Seq,GSM2696304,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696304,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D05.bam,bam,15226605.0,202462.0,GSM2696304 r1,0:37.60 1:37.61,A:4335596;C:3292087;G:3205961;T:4390270;N:2691,37,37,,,4335596,3292087,3205961,4390270,2691,SRX2989437,SRS2341360,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91107,0.91265,0.25537,0.25586,0.98443,0.98581,0.4967,0.48642,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42674,SRR5810884,SRX2989436,SRS2341359,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D04,GSM2696303,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696303,GSM2696303: rag2 GFP.P2.D04; Danio rerio; RNA Seq,GSM2696303,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696303,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D04.bam,bam,106079832.0,1411328.0,GSM2696303 r1,0:37.58 1:37.58,A:28894435;C:24306423;G:23644014;T:29214896;N:20064,37,37,,,28894435,24306423,23644014,29214896,20064,SRX2989436,SRS2341359,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9227,0.92237,0.13726,0.13735,0.9553,0.95647,0.49331,0.49947,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42675,SRR5810883,SRX2989435,SRS2341358,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D03,GSM2696302,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696302,GSM2696302: rag2 GFP.P2.D03; Danio rerio; RNA Seq,GSM2696302,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696302,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D03.bam,bam,21289941.0,283156.0,GSM2696302 r1,0:37.59 1:37.59,A:5938700;C:4726083;G:4610632;T:6010768;N:3758,37,37,,,5938700,4726083,4610632,6010768,3758,SRX2989435,SRS2341358,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91069,0.911,0.20523,0.20574,0.9825,0.98267,0.52786,0.52592,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42676,SRR5810882,SRX2989434,SRS2341356,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D02,GSM2696301,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D02,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696301,GSM2696301: rag2 GFP.P2.D02; Danio rerio; RNA Seq,GSM2696301,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696301,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D02.bam,bam,130831699.0,1740981.0,GSM2696301 r1,0:37.57 1:37.58,A:35439280;C:30110780;G:29373364;T:35882908;N:25367,37,37,,,35439280,30110780,29373364,35882908,25367,SRX2989434,SRS2341356,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91951,0.91958,0.07134,0.07239,0.95982,0.96035,0.47198,0.46193,36,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42677,SRR5810881,SRX2989433,SRS2341357,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.D01,GSM2696300,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.D01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696300,GSM2696300: rag2 GFP.P2.D01; Danio rerio; RNA Seq,GSM2696300,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696300,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.D01.bam,bam,72216876.0,960467.0,GSM2696300 r1,0:37.59 1:37.60,A:20300075;C:15865991;G:15492398;T:20545211;N:13201,37,37,,,20300075,15865991,15492398,20545211,13201,SRX2989433,SRS2341357,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91121,0.91013,0.25023,0.25089,0.98413,0.98386,0.5025,0.50723,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42678,SRR5810880,SRX2989432,SRS2341355,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C12,GSM2696299,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696299,GSM2696299: rag2 GFP.P2.C12; Danio rerio; RNA Seq,GSM2696299,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696299,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C12.bam,bam,22373523.0,297634.0,GSM2696299 r1,0:37.59 1:37.59,A:6088784;C:5104577;G:4981100;T:6194997;N:4065,37,37,,,6088784,5104577,4981100,6194997,4065,SRX2989432,SRS2341355,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91311,0.91533,0.20964,0.21002,0.9792,0.97928,0.4834,0.47212,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42679,SRR5810879,SRX2989431,SRS2341354,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C11,GSM2696298,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696298,GSM2696298: rag2 GFP.P2.C11; Danio rerio; RNA Seq,GSM2696298,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696298,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C11.bam,bam,78810745.0,1048392.0,GSM2696298 r1,0:37.59 1:37.59,A:21634279;C:17846551;G:17407357;T:21908404;N:14154,37,37,,,21634279,17846551,17407357,21908404,14154,SRX2989431,SRS2341354,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91212,0.91267,0.21149,0.21231,0.978,0.97786,0.48227,0.47875,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42680,SRR5810878,SRX2989430,SRS2341353,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C10,GSM2696297,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C10,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696297,GSM2696297: rag2 GFP.P2.C10; Danio rerio; RNA Seq,GSM2696297,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696297,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C10.bam,bam,154890779.0,2061421.0,GSM2696297 r1,0:37.57 1:37.57,A:41644375;C:35992054;G:35099983;T:42124751;N:29616,37,37,,,41644375,35992054,35099983,42124751,29616,SRX2989430,SRS2341353,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9261,0.92549,0.04577,0.04608,0.95797,0.95826,0.44523,0.46091,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42681,SRR5810877,SRX2989429,SRS2341352,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C09,GSM2696296,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C09,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696296,GSM2696296: rag2 GFP.P2.C09; Danio rerio; RNA Seq,GSM2696296,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696296,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C09.bam,bam,86053163.0,1144799.0,GSM2696296 r1,0:37.58 1:37.58,A:23469332;C:19619086;G:19128553;T:23821080;N:15112,37,37,,,23469332,19619086,19128553,23821080,15112,SRX2989429,SRS2341352,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92258,0.92166,0.17885,0.1778,0.9809,0.9807,0.51015,0.51165,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42682,SRR5810876,SRX2989428,SRS2341351,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C08,GSM2696295,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C08,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696295,GSM2696295: rag2 GFP.P2.C08; Danio rerio; RNA Seq,GSM2696295,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696295,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C08.bam,bam,118924924.0,1581653.0,GSM2696295 r1,0:37.59 1:37.60,A:33009966;C:26571079;G:25850082;T:33472830;N:20967,37,37,,,33009966,26571079,25850082,33472830,20967,SRX2989428,SRS2341351,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9157,0.91478,0.22106,0.22031,0.97589,0.97617,0.48841,0.49188,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42683,SRR5810875,SRX2989427,SRS2341350,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C07,GSM2696294,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C07,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696294,GSM2696294: rag2 GFP.P2.C07; Danio rerio; RNA Seq,GSM2696294,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696294,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C07.bam,bam,9988556.0,132843.0,GSM2696294 r1,0:37.59 1:37.60,A:2772130;C:2233647;G:2176332;T:2804570;N:1877,37,37,,,2772130,2233647,2176332,2804570,1877,SRX2989427,SRS2341350,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91186,0.91524,0.19543,0.19665,0.9805,0.98102,0.5186,0.49636,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42684,SRR5810874,SRX2989426,SRS2341348,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C06,GSM2696293,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C06,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696293,GSM2696293: rag2 GFP.P2.C06; Danio rerio; RNA Seq,GSM2696293,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696293,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C06.bam,bam,103103159.0,1371207.0,GSM2696293 r1,0:37.60 1:37.60,A:28830393;C:22847649;G:22272928;T:29134344;N:17845,37,37,,,28830393,22847649,22272928,29134344,17845,SRX2989426,SRS2341348,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91702,0.91593,0.24115,0.24155,0.97977,0.98015,0.4552,0.46694,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42685,SRR5810873,SRX2989425,SRS2341349,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C05,GSM2696292,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696292,GSM2696292: rag2 GFP.P2.C05; Danio rerio; RNA Seq,GSM2696292,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696292,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C05.bam,bam,11111536.0,147741.0,GSM2696292 r1,0:37.60 1:37.61,A:3160481;C:2407745;G:2341866;T:3199429;N:2015,37,37,,,3160481,2407745,2341866,3199429,2015,SRX2989425,SRS2341349,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.89912,0.90073,0.26875,0.26861,0.9753,0.97615,0.51894,0.51132,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42686,SRR5810872,SRX2989424,SRS2341347,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C04,GSM2696291,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696291,GSM2696291: rag2 GFP.P2.C04; Danio rerio; RNA Seq,GSM2696291,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696291,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C04.bam,bam,81184966.0,1079704.0,GSM2696291 r1,0:37.60 1:37.60,A:22543314;C:18084723;G:17672827;T:22869375;N:14727,37,37,,,22543314,18084723,17672827,22869375,14727,SRX2989424,SRS2341347,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91213,0.91247,0.24311,0.24242,0.97954,0.9796,0.50803,0.51579,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42687,SRR5810871,SRX2989423,SRS2341346,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C03,GSM2696290,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696290,GSM2696290: rag2 GFP.P2.C03; Danio rerio; RNA Seq,GSM2696290,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696290,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C03.bam,bam,28517161.0,379392.0,GSM2696290 r1,0:37.58 1:37.58,A:7727367;C:6553077;G:6380391;T:7851009;N:5317,37,37,,,7727367,6553077,6380391,7851009,5317,SRX2989423,SRS2341346,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91976,0.92184,0.16619,0.16676,0.98344,0.98364,0.51756,0.52858,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42688,SRR5810870,SRX2989422,SRS2341345,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C02,GSM2696289,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C02,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696289,GSM2696289: rag2 GFP.P2.C02; Danio rerio; RNA Seq,GSM2696289,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696289,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C02.bam,bam,64384851.0,856314.0,GSM2696289 r1,0:37.59 1:37.59,A:17799889;C:14436625;G:14070935;T:18066528;N:10874,37,37,,,17799889,14436625,14070935,18066528,10874,SRX2989422,SRS2341345,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90357,0.90266,0.20812,0.20739,0.98307,0.98334,0.51206,0.51231,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42689,SRR5810869,SRX2989421,SRS2341344,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.C01,GSM2696288,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.C01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696288,GSM2696288: rag2 GFP.P2.C01; Danio rerio; RNA Seq,GSM2696288,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696288,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.C01.bam,bam,79587566.0,1058811.0,GSM2696288 r1,0:37.58 1:37.58,A:21790575;C:18066457;G:17626457;T:22087840;N:16237,37,37,,,21790575,18066457,17626457,22087840,16237,SRX2989421,SRS2341344,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9215,0.92115,0.19713,0.19752,0.9866,0.98677,0.49777,0.49443,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42690,SRR5810868,SRX2989420,SRS2341343,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B12,GSM2696287,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696287,GSM2696287: rag2 GFP.P2.B12; Danio rerio; RNA Seq,GSM2696287,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B12.bam,bam,75747584.0,1007587.0,GSM2696287 r1,0:37.59 1:37.59,A:20851200;C:17027054;G:16642568;T:21212331;N:14431,37,37,,,20851200,17027054,16642568,21212331,14431,SRX2989420,SRS2341343,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91613,0.9161,0.24169,0.24224,0.98575,0.98614,0.46661,0.46382,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42691,SRR5810867,SRX2989419,SRS2341342,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B11,GSM2696286,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696286,GSM2696286: rag2 GFP.P2.B11; Danio rerio; RNA Seq,GSM2696286,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B11.bam,bam,77633212.0,1032483.0,GSM2696286 r1,0:37.60 1:37.60,A:21782831;C:17078949;G:16715192;T:22042402;N:13838,37,37,,,21782831,17078949,16715192,22042402,13838,SRX2989419,SRS2341342,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91306,0.91354,0.24885,0.24956,0.97871,0.97895,0.48054,0.4813,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42692,SRR5810866,SRX2989418,SRS2341340,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B10,GSM2696285,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B10,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696285,GSM2696285: rag2 GFP.P2.B10; Danio rerio; RNA Seq,GSM2696285,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696285,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B10.bam,bam,88874193.0,1182128.0,GSM2696285 r1,0:37.59 1:37.59,A:24630450;C:19861243;G:19422748;T:24943365;N:16387,37,37,,,24630450,19861243,19422748,24943365,16387,SRX2989418,SRS2341340,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91029,0.91053,0.21581,0.21529,0.98029,0.98054,0.46524,0.46835,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42693,SRR5810865,SRX2989417,SRS2341341,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B09,GSM2696284,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B09,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696284,GSM2696284: rag2 GFP.P2.B09; Danio rerio; RNA Seq,GSM2696284,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696284,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B09.bam,bam,88695036.0,1179768.0,GSM2696284 r1,0:37.59 1:37.59,A:24657110;C:19757143;G:19282829;T:24981574;N:16380,37,37,,,24657110,19757143,19282829,24981574,16380,SRX2989417,SRS2341341,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91272,0.91419,0.21612,0.21757,0.98054,0.98042,0.50929,0.51742,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42694,SRR5810864,SRX2989416,SRS2341339,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B08,GSM2696283,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B08,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696283,GSM2696283: rag2 GFP.P2.B08; Danio rerio; RNA Seq,GSM2696283,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696283,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B08.bam,bam,100397846.0,1335199.0,GSM2696283 r1,0:37.60 1:37.60,A:28095395;C:22178822;G:21634414;T:28472347;N:16868,37,37,,,28095395,22178822,21634414,28472347,16868,SRX2989416,SRS2341339,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91193,0.91122,0.24835,0.24849,0.9793,0.98007,0.51746,0.51569,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42695,SRR5810863,SRX2989415,SRS2341338,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B07,GSM2696282,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B07,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696282,GSM2696282: rag2 GFP.P2.B07; Danio rerio; RNA Seq,GSM2696282,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696282,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B07.bam,bam,63556018.0,845461.0,GSM2696282 r1,0:37.59 1:37.59,A:17653555;C:14183332;G:13842748;T:17864076;N:12307,37,37,,,17653555,14183332,13842748,17864076,12307,SRX2989415,SRS2341338,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91458,0.91516,0.19376,0.19517,0.98056,0.98119,0.49947,0.50116,37,36,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42696,SRR5810862,SRX2989414,SRS2341337,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B06,GSM2696281,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B06,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696281,GSM2696281: rag2 GFP.P2.B06; Danio rerio; RNA Seq,GSM2696281,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696281,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B06.bam,bam,111734332.0,1486425.0,GSM2696281 r1,0:37.58 1:37.59,A:30743036;C:25241084;G:24623673;T:31105737;N:20802,37,37,,,30743036,25241084,24623673,31105737,20802,SRX2989414,SRS2341337,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.92175,0.92209,0.17967,0.18055,0.97956,0.97987,0.51119,0.50576,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42697,SRR5810861,SRX2989413,SRS2341336,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B05,GSM2696280,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696280,GSM2696280: rag2 GFP.P2.B05; Danio rerio; RNA Seq,GSM2696280,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696280,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B05.bam,bam,55365225.0,736304.0,GSM2696280 r1,0:37.60 1:37.60,A:15558655;C:12177531;G:11851841;T:15766972;N:10226,37,37,,,15558655,12177531,11851841,15766972,10226,SRX2989413,SRS2341336,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91324,0.91479,0.23984,0.24099,0.97392,0.97404,0.44855,0.40641,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42698,SRR5810860,SRX2989412,SRS2341335,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B04,GSM2696279,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696279,GSM2696279: rag2 GFP.P2.B04; Danio rerio; RNA Seq,GSM2696279,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696279,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B04.bam,bam,77935622.0,1036482.0,GSM2696279 r1,0:37.60 1:37.60,A:21785803;C:17240481;G:16831609;T:22063503;N:14226,37,37,,,21785803,17240481,16831609,22063503,14226,SRX2989412,SRS2341335,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91176,0.91266,0.22117,0.2215,0.98287,0.9836,0.48496,0.48144,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42699,SRR5810859,SRX2989411,SRS2341334,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B03,GSM2696278,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696278,GSM2696278: rag2 GFP.P2.B03; Danio rerio; RNA Seq,GSM2696278,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696278,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B03.bam,bam,83103650.0,1105088.0,GSM2696278 r1,0:37.60 1:37.60,A:23839250;C:17782857;G:17400714;T:24065195;N:15634,37,37,,,23839250,17782857,17400714,24065195,15634,SRX2989411,SRS2341334,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91181,0.9099,0.27422,0.27377,0.98405,0.98417,0.42899,0.42611,36,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42700,SRR5810858,SRX2989410,SRS2341332,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B02,GSM2696277,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B02,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696277,GSM2696277: rag2 GFP.P2.B02; Danio rerio; RNA Seq,GSM2696277,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696277,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B02.bam,bam,73330904.0,975539.0,GSM2696277 r1,0:37.59 1:37.58,A:20106542;C:16631135;G:16201490;T:20377885;N:13852,37,37,,,20106542,16631135,16201490,20377885,13852,SRX2989410,SRS2341332,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91473,0.91485,0.1819,0.18233,0.97946,0.97991,0.48861,0.49736,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42701,SRR5810857,SRX2989409,SRS2341333,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.B01,GSM2696276,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.B01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696276,GSM2696276: rag2 GFP.P2.B01; Danio rerio; RNA Seq,GSM2696276,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696276,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.B01.bam,bam,104951034.0,1395782.0,GSM2696276 r1,0:37.60 1:37.60,A:29435803;C:23140910;G:22594186;T:29760946;N:19189,37,37,,,29435803,23140910,22594186,29760946,19189,SRX2989409,SRS2341333,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91294,0.91356,0.23851,0.24069,0.97473,0.97542,0.49853,0.4848,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42702,SRR5810856,SRX2989408,SRS2341331,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A12,GSM2696275,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696275,GSM2696275: rag2 GFP.P2.A12; Danio rerio; RNA Seq,GSM2696275,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696275,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A12.bam,bam,22599193.0,300648.0,GSM2696275 r1,0:37.58 1:37.59,A:6219600;C:5116034;G:4991333;T:6267653;N:4573,37,37,,,6219600,5116034,4991333,6267653,4573,SRX2989408,SRS2341331,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91397,0.91306,0.15337,0.15359,0.97617,0.97642,0.49778,0.50414,36,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42703,SRR5810855,SRX2989407,SRS2341330,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A11,GSM2696274,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696274,GSM2696274: rag2 GFP.P2.A11; Danio rerio; RNA Seq,GSM2696274,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696274,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A11.bam,bam,71541404.0,951700.0,GSM2696274 r1,0:37.59 1:37.59,A:19686321;C:16165883;G:15769214;T:19906805;N:13181,37,37,,,19686321,16165883,15769214,19906805,13181,SRX2989407,SRS2341330,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91665,0.91658,0.17218,0.17307,0.96591,0.9665,0.50094,0.49765,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42704,SRR5810854,SRX2989406,SRS2341329,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A10,GSM2696273,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A10,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696273,GSM2696273: rag2 GFP.P2.A10; Danio rerio; RNA Seq,GSM2696273,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696273,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A10.bam,bam,47412867.0,630575.0,GSM2696273 r1,0:37.60 1:37.59,A:13207226;C:10536320;G:10257941;T:13402916;N:8464,37,37,,,13207226,10536320,10257941,13402916,8464,SRX2989406,SRS2341329,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91317,0.91343,0.25264,0.25282,0.98287,0.98287,0.48839,0.4618,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42705,SRR5810853,SRX2989405,SRS2341328,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A09,GSM2696272,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A09,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696272,GSM2696272: rag2 GFP.P2.A09; Danio rerio; RNA Seq,GSM2696272,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696272,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A09.bam,bam,10646574.0,141660.0,GSM2696272 r1,0:37.58 1:37.58,A:2842805;C:2490162;G:2434224;T:2877070;N:2313,37,37,,,2842805,2490162,2434224,2877070,2313,SRX2989405,SRS2341328,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91869,0.91857,0.21282,0.21084,0.98238,0.98224,0.46759,0.46288,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42706,SRR5810852,SRX2989404,SRS2341327,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A08,GSM2696271,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A08,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696271,GSM2696271: rag2 GFP.P2.A08; Danio rerio; RNA Seq,GSM2696271,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696271,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A08.bam,bam,64474110.0,857310.0,GSM2696271 r1,0:37.60 1:37.60,A:18304777;C:13991830;G:13610941;T:18555323;N:11239,37,37,,,18304777,13991830,13610941,18555323,11239,SRX2989404,SRS2341327,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9021,0.90521,0.23914,0.23912,0.97743,0.97826,0.48887,0.48194,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42707,SRR5810851,SRX2989403,SRS2341326,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A07,GSM2696270,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A07,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696270,GSM2696270: rag2 GFP.P2.A07; Danio rerio; RNA Seq,GSM2696270,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696270,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A07.bam,bam,26843949.0,357197.0,GSM2696270 r1,0:37.57 1:37.58,A:7164024;C:6280927;G:6136127;T:7257448;N:5423,37,37,,,7164024,6280927,6136127,7257448,5423,SRX2989403,SRS2341326,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91775,0.9184,0.17313,0.17239,0.98443,0.98441,0.49289,0.49601,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42708,SRR5810850,SRX2989402,SRS2341325,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A06,GSM2696269,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A06,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696269,GSM2696269: rag2 GFP.P2.A06; Danio rerio; RNA Seq,GSM2696269,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696269,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A06.bam,bam,81633753.0,1085845.0,GSM2696269 r1,0:37.59 1:37.59,A:22696781;C:18204239;G:17754652;T:22963563;N:14518,37,37,,,22696781,18204239,17754652,22963563,14518,SRX2989402,SRS2341325,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91583,0.91555,0.21602,0.21589,0.97887,0.97946,0.49817,0.50035,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42709,SRR5810849,SRX2989401,SRS2341324,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A05,GSM2696268,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696268,GSM2696268: rag2 GFP.P2.A05; Danio rerio; RNA Seq,GSM2696268,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696268,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A05.bam,bam,35023700.0,465868.0,GSM2696268 r1,0:37.59 1:37.59,A:9607520;C:7930335;G:7728004;T:9750859;N:6982,37,37,,,9607520,7930335,7728004,9750859,6982,SRX2989401,SRS2341324,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91301,0.91475,0.17681,0.17622,0.98098,0.98202,0.49031,0.50687,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42710,SRR5810848,SRX2989400,SRS2341323,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A04,GSM2696267,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696267,GSM2696267: rag2 GFP.P2.A04; Danio rerio; RNA Seq,GSM2696267,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696267,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A04.bam,bam,85688896.0,1139957.0,GSM2696267 r1,0:37.58 1:37.58,A:23410108;C:19473305;G:18993094;T:23796160;N:16229,37,37,,,23410108,19473305,18993094,23796160,16229,SRX2989400,SRS2341323,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9119,0.91255,0.19097,0.19074,0.97966,0.97964,0.49112,0.50759,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42711,SRR5810847,SRX2989399,SRS2341322,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A03,GSM2696266,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696266,GSM2696266: rag2 GFP.P2.A03; Danio rerio; RNA Seq,GSM2696266,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696266,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A03.bam,bam,16108084.0,214228.0,GSM2696266 r1,0:37.60 1:37.60,A:4477688;C:3596401;G:3506830;T:4524163;N:3002,37,37,,,4477688,3596401,3506830,4524163,3002,SRX2989399,SRS2341322,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90174,0.89952,0.19264,0.19298,0.98123,0.98139,0.49586,0.49713,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42712,SRR5810846,SRX2989398,SRS2341321,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A02,GSM2696265,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A02,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696265,GSM2696265: rag2 GFP.P2.A02; Danio rerio; RNA Seq,GSM2696265,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696265,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A02.bam,bam,46275671.0,615474.0,GSM2696265 r1,0:37.59 1:37.59,A:12856259;C:10315027;G:10057437;T:13038218;N:8730,37,37,,,12856259,10315027,10057437,13038218,8730,SRX2989398,SRS2341321,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91688,0.91519,0.2284,0.22838,0.98127,0.98179,0.48304,0.47736,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42713,SRR5810845,SRX2989397,SRS2341320,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,rag2 GFP.P2.A01,GSM2696264,,source name:whole kidney marrow|tissue:kidney marrow,rag2 GFP.P2.A01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696264,GSM2696264: rag2 GFP.P2.A01; Danio rerio; RNA Seq,GSM2696264,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696264,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,rag2_GFP.P2.A01.bam,bam,23477058.0,312166.0,GSM2696264 r1,0:37.60 1:37.60,A:6659006;C:5095262;G:4985498;T:6733081;N:4211,37,37,,,6659006,5095262,4985498,6733081,4211,SRX2989397,SRS2341320,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9131,0.9128,0.29453,0.29564,0.9752,0.97613,0.53106,0.52067,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42714,SRR5810844,SRX2989396,SRS2341319,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H12,GSM2696263,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696263,GSM2696263: mpx EGFP.P4.H12; Danio rerio; RNA Seq,GSM2696263,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696263,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H12.bam,bam,32176246.0,428001.0,GSM2696263 r1,0:37.59 1:37.59,A:8909175;C:7207825;G:7042822;T:9010633;N:5791,37,37,,,8909175,7207825,7042822,9010633,5791,SRX2989396,SRS2341319,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91167,0.91143,0.15174,0.15251,0.95948,0.96047,0.42458,0.42532,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42715,SRR5810843,SRX2989395,SRS2341318,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H11,GSM2696262,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696262,GSM2696262: mpx EGFP.P4.H11; Danio rerio; RNA Seq,GSM2696262,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696262,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H11.bam,bam,19724647.0,262274.0,GSM2696262 r1,0:37.60 1:37.60,A:5576081;C:4315954;G:4196441;T:5632827;N:3344,37,37,,,5576081,4315954,4196441,5632827,3344,SRX2989395,SRS2341318,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90822,0.91067,0.16746,0.16672,0.96721,0.96704,0.40809,0.42507,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42716,SRR5810842,SRX2989394,SRS2341317,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H10,GSM2696261,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H10,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696261,GSM2696261: mpx EGFP.P4.H10; Danio rerio; RNA Seq,GSM2696261,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696261,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H10.bam,bam,55835754.0,742846.0,GSM2696261 r1,0:37.58 1:37.58,A:15148584;C:12815575;G:12510744;T:15350082;N:10769,37,37,,,15148584,12815575,12510744,15350082,10769,SRX2989394,SRS2341317,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9212,0.92006,0.11689,0.11621,0.95266,0.95339,0.46277,0.44994,37,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42717,SRR5810841,SRX2989393,SRS2341316,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H09,GSM2696260,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H09,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696260,GSM2696260: mpx EGFP.P4.H09; Danio rerio; RNA Seq,GSM2696260,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696260,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H09.bam,bam,22785484.0,303075.0,GSM2696260 r1,0:37.59 1:37.59,A:6369221;C:5055762;G:4943016;T:6413193;N:4292,37,37,,,6369221,5055762,4943016,6413193,4292,SRX2989393,SRS2341316,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90539,0.9055,0.134,0.13358,0.97064,0.97177,0.4445,0.43086,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42718,SRR5810840,SRX2989392,SRS2341315,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H08,GSM2696259,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H08,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696259,GSM2696259: mpx EGFP.P4.H08; Danio rerio; RNA Seq,GSM2696259,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696259,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H08.bam,bam,39958695.0,531435.0,GSM2696259 r1,0:37.60 1:37.59,A:11202583;C:8832494;G:8618616;T:11297654;N:7348,37,37,,,11202583,8832494,8618616,11297654,7348,SRX2989392,SRS2341315,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.9151,0.91394,0.17352,0.17405,0.96848,0.96946,0.44777,0.42759,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42719,SRR5810839,SRX2989391,SRS2341313,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H07,GSM2696258,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H07,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696258,GSM2696258: mpx EGFP.P4.H07; Danio rerio; RNA Seq,GSM2696258,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696258,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H07.bam,bam,37265166.0,495664.0,GSM2696258 r1,0:37.59 1:37.59,A:10372583;C:8317319;G:8103545;T:10464755;N:6964,37,37,,,10372583,8317319,8103545,10464755,6964,SRX2989391,SRS2341313,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91982,0.92098,0.15292,0.15262,0.96461,0.9656,0.4249,0.4294,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42720,SRR5810838,SRX2989390,SRS2341314,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H06,GSM2696257,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H06,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696257,GSM2696257: mpx EGFP.P4.H06; Danio rerio; RNA Seq,GSM2696257,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696257,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H06.bam,bam,45219191.0,601480.0,GSM2696257 r1,0:37.59 1:37.59,A:12521302;C:10156138;G:9902690;T:12630774;N:8287,37,37,,,12521302,10156138,9902690,12630774,8287,SRX2989390,SRS2341314,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91858,0.91783,0.13125,0.13092,0.96303,0.96374,0.41518,0.41356,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42721,SRR5810837,SRX2989389,SRS2341312,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H05,GSM2696256,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H05,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696256,GSM2696256: mpx EGFP.P4.H05; Danio rerio; RNA Seq,GSM2696256,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696256,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H05.bam,bam,34158393.0,454274.0,GSM2696256 r1,0:37.60 1:37.60,A:9622033;C:7515993;G:7328847;T:9685005;N:6515,37,37,,,9622033,7515993,7328847,9685005,6515,SRX2989389,SRS2341312,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90833,0.90833,0.18271,0.18494,0.95631,0.95757,0.43708,0.43855,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42722,SRR5810836,SRX2989388,SRS2341311,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H04,GSM2696255,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H04,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696255,GSM2696255: mpx EGFP.P4.H04; Danio rerio; RNA Seq,GSM2696255,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696255,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H04.bam,bam,36572274.0,486324.0,GSM2696255 r1,0:37.60 1:37.60,A:10367431;C:7969597;G:7782097;T:10446714;N:6435,37,37,,,10367431,7969597,7782097,10446714,6435,SRX2989388,SRS2341311,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90501,0.90543,0.2075,0.2077,0.9712,0.9712,0.48174,0.48806,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42723,SRR5810835,SRX2989387,SRS2341310,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H03,GSM2696254,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H03,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696254,GSM2696254: mpx EGFP.P4.H03; Danio rerio; RNA Seq,GSM2696254,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696254,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H03.bam,bam,23723245.0,315454.0,GSM2696254 r1,0:37.60 1:37.60,A:6762477;C:5138945;G:5002722;T:6814975;N:4126,37,37,,,6762477,5138945,5002722,6814975,4126,SRX2989387,SRS2341310,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.90392,0.90434,0.21502,0.21597,0.97189,0.9726,0.45016,0.4616,38,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42724,SRR5810834,SRX2989386,SRS2341309,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.H01,GSM2696253,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.H01,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696253,GSM2696253: mpx EGFP.P4.H01; Danio rerio; RNA Seq,GSM2696253,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696253,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.H01.bam,bam,80550728.0,1071618.0,GSM2696253 r1,0:37.58 1:37.58,A:22059215;C:18284299;G:17901368;T:22290753;N:15093,37,37,,,22059215,18284299,17901368,22290753,15093,SRX2989386,SRS2341309,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91556,0.91518,0.14017,0.14014,0.94927,0.94949,0.46114,0.46206,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42725,SRR5810833,SRX2989385,SRS2341308,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.G12,GSM2696252,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.G12,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696252,GSM2696252: mpx EGFP.P4.G12; Danio rerio; RNA Seq,GSM2696252,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696252,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.G12.bam,bam,28392785.0,377627.0,GSM2696252 r1,0:37.59 1:37.60,A:7913053;C:6326391;G:6143700;T:8004704;N:4937,37,37,,,7913053,6326391,6143700,8004704,4937,SRX2989385,SRS2341308,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91503,0.91691,0.14281,0.14234,0.96345,0.96303,0.42128,0.43377,37,38,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42726,SRR5810832,SRX2989384,SRS2341306,SRP111340,PRJNA393431,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq],GSE100911,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,,mpx EGFP.P4.G11,GSM2696251,,source name:whole kidney marrow|tissue:kidney marrow,mpx EGFP.P4.G11,Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts,whole kidney marrow,,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,,tissue:kidney marrow,GSM2696251,GSM2696251: mpx EGFP.P4.G11; Danio rerio; RNA Seq,GSM2696251,,1,Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.,GEO Accession:GSM2696251,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP111340,,,mpx_EGFP.P4.G11.bam,bam,26010864.0,345914.0,GSM2696251 r1,0:37.60 1:37.60,A:7319775;C:5721636;G:5574657;T:7390036;N:4760,37,37,,,7319775,5721636,5574657,7390036,4760,SRX2989384,SRS2341306,SRA584588,GEO,"Pathology, Massachusetts General Hospital",2,0.91164,0.91038,0.1508,0.14942,0.96195,0.96266,0.43082,0.44168,38,37,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System