metadata: run_metadata: 261 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "smartseq" and tissue

261 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "smartseq" and tissue_curation = "Kidney"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
42627	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;