metadata: run_metadata: 47 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue

47 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" 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.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.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
64483	64483	SRR14713035	SRX11050991	SRS9118959	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 heterozygous [het2]	GSM5353444	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	runx1 heterozygous [het2]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	GSM5353444	GSM5353444: runx1 heterozygous [het2]; Danio rerio; RNA Seq	GSM5353444		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353444	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=het2 S3 L001 I1 001.fastq.gz read2PairFiles=het2 S3 L001 R1 001.fastq.gz read3PairFiles=het2 S3 L001 R2 001.fastq.gz	het2_S3_L001_I1_001.fastq.gz het2_S3_L001_R1_001.fastq.gz het2_S3_L001_R2_001.fastq.gz	fastq fastq fastq	15663557054.0	124177953.0	GSM5353444 r1	0:8 1:27.58 2:90.56	A:3222090217;C:2457731774;G:2657226801;T:2906730616;N:1348005	8	27	90	3222090217	2457731774	2657226801	2906730616	1348005	SRX11050991	SRS9118959	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.93627		0.12855		0.80722		0.53604		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64484	64484	SRR14713036	SRX11050991	SRS9118959	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 heterozygous [het2]	GSM5353444	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	runx1 heterozygous [het2]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	GSM5353444	GSM5353444: runx1 heterozygous [het2]; Danio rerio; RNA Seq	GSM5353444		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353444	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=het2 S3 L002 I1 001.fastq.gz read2PairFiles=het2 S3 L002 R1 001.fastq.gz read3PairFiles=het2 S3 L002 R2 001.fastq.gz	het2_S3_L002_I1_001.fastq.gz het2_S3_L002_R1_001.fastq.gz het2_S3_L002_R2_001.fastq.gz	fastq fastq fastq	15733917976.0	124735364.0	GSM5353444 r2	0:8 1:27.58 2:90.56	A:3236625131;C:2468696674;G:2669813570;T:2919169352;N:1355273	8	27	90	3236625131	2468696674	2669813570	2919169352	1355273	SRX11050991	SRS9118959	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.93597		0.12775		0.80872		0.52945		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64485	64485	SRR14713033	SRX11050990	SRS9118958	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 heterozygous [het1]	GSM5353443	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	runx1 heterozygous [het1]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	GSM5353443	GSM5353443: runx1 heterozygous [het1]; Danio rerio; RNA Seq	GSM5353443		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353443	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=het1 S1 L001 I1 001.fastq.gz read2PairFiles=het1 S1 L001 R1 001.fastq.gz read3PairFiles=het1 S1 L001 R2 001.fastq.gz	het1_S1_L001_I1_001.fastq.gz het1_S1_L001_R1_001.fastq.gz het1_S1_L001_R2_001.fastq.gz	fastq fastq fastq	14144386609.0	112134541.0	GSM5353443 r1	0:8 1:27.58 2:90.56	A:2911415156;C:2232516450;G:2400128566;T:2609309040;N:1216894	8	27	90	2911415156	2232516450	2400128566	2609309040	1216894	SRX11050990	SRS9118958	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.93943		0.1263		0.81055		0.54188		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64486	64486	SRR14713034	SRX11050990	SRS9118958	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 heterozygous [het1]	GSM5353443	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	runx1 heterozygous [het1]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	GSM5353443	GSM5353443: runx1 heterozygous [het1]; Danio rerio; RNA Seq	GSM5353443		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353443	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=het1 S1 L002 I1 001.fastq.gz read2PairFiles=het1 S1 L002 R1 001.fastq.gz read3PairFiles=het1 S1 L002 R2 001.fastq.gz	het1_S1_L002_I1_001.fastq.gz het1_S1_L002_R1_001.fastq.gz het1_S1_L002_R2_001.fastq.gz	fastq fastq fastq	14198963993.0	112567012.0	GSM5353443 r2	0:8 1:27.58 2:90.56	A:2922564124;C:2241222197;G:2410043722;T:2618704172;N:1244941	8	27	90	2922564124	2241222197	2410043722	2618704172	1244941	SRX11050990	SRS9118958	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.93945		0.1279		0.81205		0.54199		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64487	64487	SRR14713047	SRX11050989	SRS9118957	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 homozygous [ko4]	GSM5353450	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	runx1 homozygous [ko4]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	GSM5353450	GSM5353450: runx1 homozygous [ko4]; Danio rerio; RNA Seq	GSM5353450		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353450	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ko4 S8 L001 I1 001.fastq.gz read2PairFiles=ko4 S8 L001 R1 001.fastq.gz read3PairFiles=ko4 S8 L001 R2 001.fastq.gz	ko4_S8_L001_I1_001.fastq.gz ko4_S8_L001_R1_001.fastq.gz ko4_S8_L001_R2_001.fastq.gz	fastq fastq fastq	13992524630.0	110906152.0	GSM5353450 r1	0:8 1:27.58 2:90.58	A:2982262991;C:2094207271;G:2250607795;T:2718018274;N:1209671	8	27	90	2982262991	2094207271	2250607795	2718018274	1209671	SRX11050989	SRS9118957	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.91453		0.21027		0.7724		0.60148		88		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64488	64488	SRR14713048	SRX11050989	SRS9118957	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 homozygous [ko4]	GSM5353450	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	runx1 homozygous [ko4]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	GSM5353450	GSM5353450: runx1 homozygous [ko4]; Danio rerio; RNA Seq	GSM5353450		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353450	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ko4 S8 L002 I1 001.fastq.gz read2PairFiles=ko4 S8 L002 R1 001.fastq.gz read3PairFiles=ko4 S8 L002 R2 001.fastq.gz	ko4_S8_L002_I1_001.fastq.gz ko4_S8_L002_R1_001.fastq.gz ko4_S8_L002_R2_001.fastq.gz	fastq fastq fastq	14045176738.0	111323195.0	GSM5353450 r2	0:8 1:27.58 2:90.58	A:2993422870;C:2102123853;G:2259649775;T:2727701329;N:1220191	8	27	90	2993422870	2102123853	2259649775	2727701329	1220191	SRX11050989	SRS9118957	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.91368		0.21103		0.77305		0.57218		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64489	64489	SRR14713045	SRX11050988	SRS9118956	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 homozygous [ko3]	GSM5353449	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	runx1 homozygous [ko3]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	GSM5353449	GSM5353449: runx1 homozygous [ko3]; Danio rerio; RNA Seq	GSM5353449		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353449	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ko3 S6 L001 I1 001.fastq.gz read2PairFiles=ko3 S6 L001 R1 001.fastq.gz read3PairFiles=ko3 S6 L001 R2 001.fastq.gz	ko3_S6_L001_I1_001.fastq.gz ko3_S6_L001_R1_001.fastq.gz ko3_S6_L001_R2_001.fastq.gz	fastq fastq fastq	18568439982.0	147229230.0	GSM5353449 r1	0:8 1:27.58 2:90.54	A:3724341578;C:3019598344;G:3052550431;T:3531772926;N:1597889	8	27	90	3724341578	3019598344	3052550431	3531772926	1597889	SRX11050988	SRS9118956	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94548		0.14556		0.80939		0.56646		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64490	64490	SRR14713046	SRX11050988	SRS9118956	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 homozygous [ko3]	GSM5353449	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	runx1 homozygous [ko3]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	GSM5353449	GSM5353449: runx1 homozygous [ko3]; Danio rerio; RNA Seq	GSM5353449		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353449	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ko3 S6 L002 I1 001.fastq.gz read2PairFiles=ko3 S6 L002 R1 001.fastq.gz read3PairFiles=ko3 S6 L002 R2 001.fastq.gz	ko3_S6_L002_I1_001.fastq.gz ko3_S6_L002_R1_001.fastq.gz ko3_S6_L002_R2_001.fastq.gz	fastq fastq fastq	18641428578.0	147807474.0	GSM5353449 r2	0:8 1:27.58 2:90.54	A:3738835103;C:3031462473;G:3065268246;T:3545053140;N:1634465	8	27	90	3738835103	3031462473	3065268246	3545053140	1634465	SRX11050988	SRS9118956	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94636		0.1465		0.80872		0.56839		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64491	64491	SRR14713043	SRX11050987	SRS9118955	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 homozygous [ko2]	GSM5353448	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	runx1 homozygous [ko2]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	GSM5353448	GSM5353448: runx1 homozygous [ko2]; Danio rerio; RNA Seq	GSM5353448		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353448	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ko2 S4 L001 I1 001.fastq.gz read2PairFiles=ko2 S4 L001 R1 001.fastq.gz read3PairFiles=ko2 S4 L001 R2 001.fastq.gz	ko2_S4_L001_I1_001.fastq.gz ko2_S4_L001_R1_001.fastq.gz ko2_S4_L001_R2_001.fastq.gz	fastq fastq fastq	13583701065.0	107729773.0	GSM5353448 r1	0:8 1:27.58 2:90.51	A:2614328803;C:2312765627;G:2286840395;T:2535315224;N:1170326	8	27	90	2614328803	2312765627	2286840395	2535315224	1170326	SRX11050987	SRS9118955	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9521		0.10164		0.83282		0.53497		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64492	64492	SRR14713044	SRX11050987	SRS9118955	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 homozygous [ko2]	GSM5353448	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	runx1 homozygous [ko2]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	GSM5353448	GSM5353448: runx1 homozygous [ko2]; Danio rerio; RNA Seq	GSM5353448		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353448	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ko2 S4 L002 I1 001.fastq.gz read2PairFiles=ko2 S4 L002 R1 001.fastq.gz read3PairFiles=ko2 S4 L002 R2 001.fastq.gz	ko2_S4_L002_I1_001.fastq.gz ko2_S4_L002_R1_001.fastq.gz ko2_S4_L002_R2_001.fastq.gz	fastq fastq fastq	13638926054.0	108167655.0	GSM5353448 r2	0:8 1:27.58 2:90.51	A:2624803921;C:2322432212;G:2296753639;T:2544868462;N:1185166	8	27	90	2624803921	2322432212	2296753639	2544868462	1185166	SRX11050987	SRS9118955	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9514		0.10219		0.83402		0.52448		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64493	64493	SRR14713041	SRX11050986	SRS9118954	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 homozygous [ko1]	GSM5353447	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	runx1 homozygous [ko1]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	GSM5353447	GSM5353447: runx1 homozygous [ko1]; Danio rerio; RNA Seq	GSM5353447		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353447	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ko1 S2 L001 I1 001.fastq.gz read2PairFiles=ko1 S2 L001 R1 001.fastq.gz read3PairFiles=ko1 S2 L001 R2 001.fastq.gz	ko1_S2_L001_I1_001.fastq.gz ko1_S2_L001_R1_001.fastq.gz ko1_S2_L001_R2_001.fastq.gz	fastq fastq fastq	13413711982.0	106340120.0	GSM5353447 r1	0:8 1:27.58 2:90.56	A:2784868205;C:2152619974;G:2140694771;T:2550343959;N:1164507	8	27	90	2784868205	2152619974	2140694771	2550343959	1164507	SRX11050986	SRS9118954	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94101		0.13573		0.80452		0.63043		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64494	64494	SRR14713042	SRX11050986	SRS9118954	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 homozygous [ko1]	GSM5353447	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	runx1 homozygous [ko1]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 homozygous	GSM5353447	GSM5353447: runx1 homozygous [ko1]; Danio rerio; RNA Seq	GSM5353447		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353447	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ko1 S2 L002 I1 001.fastq.gz read2PairFiles=ko1 S2 L002 R1 001.fastq.gz read3PairFiles=ko1 S2 L002 R2 001.fastq.gz	ko1_S2_L002_I1_001.fastq.gz ko1_S2_L002_R1_001.fastq.gz ko1_S2_L002_R2_001.fastq.gz	fastq fastq fastq	13469390045.0	106781267.0	GSM5353447 r2	0:8 1:27.58 2:90.56	A:2796457564;C:2161673052;G:2149962960;T:2560388359;N:1176283	8	27	90	2796457564	2161673052	2149962960	2560388359	1176283	SRX11050986	SRS9118954	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94226		0.13504		0.80474		0.55557		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64495	64495	SRR14713039	SRX11050985	SRS9118953	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 heterozygous [het4]	GSM5353446	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	runx1 heterozygous [het4]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	GSM5353446	GSM5353446: runx1 heterozygous [het4]; Danio rerio; RNA Seq	GSM5353446		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353446	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=het4 S7 L001 I1 001.fastq.gz read2PairFiles=het4 S7 L001 R1 001.fastq.gz read3PairFiles=het4 S7 L001 R2 001.fastq.gz	het4_S7_L001_I1_001.fastq.gz het4_S7_L001_R1_001.fastq.gz het4_S7_L001_R2_001.fastq.gz	fastq fastq fastq	14439557666.0	114492061.0	GSM5353446 r1	0:8 1:27.58 2:90.53	A:2881879087;C:2363134128;G:2454028728;T:2665247080;N:1231872	8	27	90	2881879087	2363134128	2454028728	2665247080	1231872	SRX11050985	SRS9118953	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94724		0.10407		0.81933		0.54039		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64496	64496	SRR14713040	SRX11050985	SRS9118953	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 heterozygous [het4]	GSM5353446	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	runx1 heterozygous [het4]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	GSM5353446	GSM5353446: runx1 heterozygous [het4]; Danio rerio; RNA Seq	GSM5353446		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353446	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=het4 S7 L002 I1 001.fastq.gz read2PairFiles=het4 S7 L002 R1 001.fastq.gz read3PairFiles=het4 S7 L002 R2 001.fastq.gz	het4_S7_L002_I1_001.fastq.gz het4_S7_L002_R1_001.fastq.gz het4_S7_L002_R2_001.fastq.gz	fastq fastq fastq	14516825269.0	115104734.0	GSM5353446 r2	0:8 1:27.58 2:90.53	A:2897098851;C:2375923349;G:2467885484;T:2678832367;N:1255959	8	27	90	2897098851	2375923349	2467885484	2678832367	1255959	SRX11050985	SRS9118953	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94771		0.1046		0.81815		0.54278		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64497	64497	SRR14713037	SRX11050984	SRS9118952	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 heterozygous [het3]	GSM5353445	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	runx1 heterozygous [het3]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	GSM5353445	GSM5353445: runx1 heterozygous [het3]; Danio rerio; RNA Seq	GSM5353445		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353445	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=het3 S5 L001 I1 001.fastq.gz read2PairFiles=het3 S5 L001 R1 001.fastq.gz read3PairFiles=het3 S5 L001 R2 001.fastq.gz	het3_S5_L001_I1_001.fastq.gz het3_S5_L001_R1_001.fastq.gz het3_S5_L001_R2_001.fastq.gz	fastq fastq fastq	17042594115.0	135113383.0	GSM5353445 r1	0:8 1:27.58 2:90.55	A:3495680489;C:2705535785;G:2814514030;T:3217929561;N:1467829	8	27	90	3495680489	2705535785	2814514030	3217929561	1467829	SRX11050984	SRS9118952	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9429		0.13005		0.80521		0.58007		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
64498	64498	SRR14713038	SRX11050984	SRS9118952	SRP322388	PRJNA734619	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II]	GSE176036	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.	parent bioproject:PRJNA734615	pubmed:34735227	runx1 heterozygous [het3]	GSM5353445	tissue:unsorted whole kidney marrow cells\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	runx1 heterozygous [het3]	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.	unsorted whole kidney marrow cells	No additional treatment for unsorted cells.	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 month\|genotype:runx1 heterozygous	GSM5353445	GSM5353445: runx1 heterozygous [het3]; Danio rerio; RNA Seq	GSM5353445		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.	GEO Accession:GSM5353445	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP322388	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=het3 S5 L002 I1 001.fastq.gz read2PairFiles=het3 S5 L002 R1 001.fastq.gz read3PairFiles=het3 S5 L002 R2 001.fastq.gz	het3_S5_L002_I1_001.fastq.gz het3_S5_L002_R1_001.fastq.gz het3_S5_L002_R2_001.fastq.gz	fastq fastq fastq	17107136510.0	135624932.0	GSM5353445 r2	0:8 1:27.58 2:90.55	A:3508835537;C:2715993447;G:2825882388;T:3229265829;N:1498996	8	27	90	3508835537	2715993447	2825882388	3229265829	1498996	SRX11050984	SRS9118952	SRA1239845	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94177		0.13016		0.80393		0.57731		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-02	Adult	Adult	Kidney	Renal System
65966	65966	SRR15712664	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-1_S1_L004_R1_001.fastq.gz six2_rds-1_S1_L004_R2_001.fastq.gz	fastq fastq	19349955000.0	64499850.0	GSM5556587 r1	0:150 1:150	A:7162489449;C:3375746042;G:3279440705;T:5531862071;N:416733	150	150		7162489449	3375746042	3279440705	5531862071	416733	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87809	0.0	0.21463	1.0	0.79689		0.57444	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65967	65967	SRR15712665	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-8_S1_L003_R1_001.fastq.gz six2_rds-8_S1_L003_R2_001.fastq.gz	fastq fastq	7105754400.0	23685848.0	GSM5556587 r10	0:150 1:150	A:2387232028;C:1255873597;G:1185129014;T:2277402001;N:117760	150	150		2387232028	1255873597	1185129014	2277402001	117760	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87582	0.0	0.20979	1.0	0.79782		0.57685	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65968	65968	SRR15712666	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-10_S1_L004_R1_001.fastq.gz six2_rds-10_S1_L004_R2_001.fastq.gz	fastq fastq	16440541800.0	54801806.0	GSM5556587 r11	0:150 1:150	A:6463236336;C:2798496412;G:2707975748;T:4470288383;N:544921	150	150		6463236336	2798496412	2707975748	4470288383	544921	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87902	0.0	0.21509	1.0	0.79395		0.56582	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65969	65969	SRR15712667	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-12_S1_L004_R1_001.fastq.gz six2_rds-12_S1_L004_R2_001.fastq.gz	fastq fastq	13212121800.0	44040406.0	GSM5556587 r12	0:150 1:150	A:5196898881;C:2253733071;G:2178536712;T:3582512811;N:440325	150	150		5196898881	2253733071	2178536712	3582512811	440325	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87751	0.0	0.21742	1.0	0.79555		0.57537	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65970	65970	SRR15712668	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-5_S1_L003_R1_001.fastq.gz six2_rds-5_S1_L003_R2_001.fastq.gz	fastq fastq	4853709900.0	16179033.0	GSM5556587 r2	0:150 1:150	A:1629549441;C:854657489;G:808913312;T:1560509625;N:80033	150	150		1629549441	854657489	808913312	1560509625	80033	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87494	0.0	0.2093	1.0	0.79732		0.57664	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65971	65971	SRR15712669	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-6_S1_L003_R1_001.fastq.gz six2_rds-6_S1_L003_R2_001.fastq.gz	fastq fastq	4426652700.0	14755509.0	GSM5556587 r3	0:150 1:150	A:1488160218;C:776137895;G:733825816;T:1428454088;N:74683	150	150		1488160218	776137895	733825816	1428454088	74683	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87652	0.0	0.21116	1.0	0.79683		0.56354	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65972	65972	SRR15712670	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-7_S1_L003_R1_001.fastq.gz six2_rds-7_S1_L003_R2_001.fastq.gz	fastq fastq	5590773600.0	18635912.0	GSM5556587 r4	0:150 1:150	A:1874947755;C:993323119;G:937833797;T:1784578957;N:89972	150	150		1874947755	993323119	937833797	1784578957	89972	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87537	0.0	0.20998	1.0	0.79709		0.57129	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65973	65973	SRR15712671	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-4_S1_L004_R1_001.fastq.gz six2_rds-4_S1_L004_R2_001.fastq.gz	fastq fastq	27727785600.0	92425952.0	GSM5556587 r5	0:150 1:150	A:10270684071;C:4847064738;G:4699231120;T:7910210723;N:594948	150	150		10270684071	4847064738	4699231120	7910210723	594948	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87788	0.0	0.2132	1.0	0.7964		0.5547	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65974	65974	SRR15712672	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-9_S1_L004_R1_001.fastq.gz six2_rds-9_S1_L004_R2_001.fastq.gz	fastq fastq	10680994800.0	35603316.0	GSM5556587 r6	0:150 1:150	A:4185708484;C:1812781715;G:1759282524;T:2922861803;N:360274	150	150		4185708484	1812781715	1759282524	2922861803	360274	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87846	0.0	0.21877	1.0	0.79462		0.54801	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65975	65975	SRR15712673	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-2_S1_L004_R1_001.fastq.gz six2_rds-2_S1_L004_R2_001.fastq.gz	fastq fastq	18583908600.0	61946362.0	GSM5556587 r7	0:150 1:150	A:6877604898;C:3234678896;G:3142926939;T:5328297692;N:400175	150	150		6877604898	3234678896	3142926939	5328297692	400175	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87774	0.0	0.2132	1.0	0.79691		0.57302	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65976	65976	SRR15712674	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-3_S1_L004_R1_001.fastq.gz six2_rds-3_S1_L004_R2_001.fastq.gz	fastq fastq	21811253100.0	72704177.0	GSM5556587 r8	0:150 1:150	A:8074244881;C:3827725258;G:3708040652;T:6200771782;N:470527	150	150		8074244881	3827725258	3708040652	6200771782	470527	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87572	0.0	0.2138	1.0	0.79989		0.5431	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
65977	65977	SRR15712675	SRX12008335	SRS10014485	SRP335554	PRJNA760458	adult zebrafish kidney cells	GSE183382	Other	To illustrate the functions of the various cell types in the zebrafish kidney we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells		pubmed:36645741	zebrafish kidney cells	GSM5556587	source name:adult zebrafish kedney cells\|strain:AB\|tissue:kidney\|developmental stage:6 month	zebrafish kidney cells	Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data dimensionality reduction clustering differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene	adult zebrafish kedney cells		Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics	Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily	strain:AB\|tissue:kidney\|developmental stage:6 month	GSM5556587	GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq	GSM5556587		1	Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics	GEO Accession:GSM5556587	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP335554		six2_rds-11_S1_L004_R1_001.fastq.gz six2_rds-11_S1_L004_R2_001.fastq.gz	fastq fastq	11680783800.0	38935946.0	GSM5556587 r9	0:150 1:150	A:4586348762;C:1986953331;G:1925942390;T:3181153183;N:386134	150	150		4586348762	1986953331	1925942390	3181153183	386134	SRX12008335	SRS10014485	SRA1288506	GEO	Xinqiao Hospital, Army Medical University (Third Military Medical University)	2	0.0	0.87701	0.0	0.21502	1.0	0.79703		0.57704	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-09-03	Adult	Adult	Kidney	Renal System
67709	67709	SRR17247457	SRX13426490	SRS11327478	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish nov2019 mcs 2	GSM5737714	source name:zebrafish kidney marrow\|Stage:adult\|class:mcs/control\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish nov2019 mcs 2	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:mcs/control\|tissue:kidney marrow	GSM5737714	GSM5737714: zfish nov2019 mcs 2; Danio rerio; RNA Seq	GSM5737714 r1	GSM5737714	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		m_2_S4_L001_R1_001.fastq.gz m_2_S4_L001_R2_001.fastq.gz	fastq fastq	30896010944.0	102304672.0	GSM5737714 r1	0:151 1:151	A:7831986052;C:6707621804;G:6407553174;T:9948342840;N:507074	151	151		7831986052	6707621804	6407553174	9948342840	507074	SRX13426490	SRS11327478	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.0362	0.95501	0.00505	0.13634	0.9978	0.87235	0.71964	0.7275	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67710	67710	SRR17247458	SRX13426490	SRS11327478	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish nov2019 mcs 2	GSM5737714	source name:zebrafish kidney marrow\|Stage:adult\|class:mcs/control\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish nov2019 mcs 2	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:mcs/control\|tissue:kidney marrow	GSM5737714	GSM5737714: zfish nov2019 mcs 2; Danio rerio; RNA Seq	GSM5737714 r1	GSM5737714	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		m_2_S4_L002_R1_001.fastq.gz m_2_S4_L002_R2_001.fastq.gz	fastq fastq	31427224716.0	104063658.0	GSM5737714 r2	0:151 1:151	A:7951620974;C:6826123654;G:6471292663;T:10177703459;N:483966	151	151		7951620974	6826123654	6471292663	10177703459	483966	SRX13426490	SRS11327478	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.03694	0.95444	0.00516	0.13567	0.99734	0.87326	0.75563	0.74575	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67711	67711	SRR17247459	SRX13426489	SRS11327476	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish nov2019 mcs 1	GSM5737713	source name:zebrafish kidney marrow\|Stage:adult\|class:mcs/control\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish nov2019 mcs 1	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:mcs/control\|tissue:kidney marrow	GSM5737713	GSM5737713: zfish nov2019 mcs 1; Danio rerio; RNA Seq	GSM5737713 r1	GSM5737713	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		m_1_S3_L001_R1_001.fastq.gz m_1_S3_L001_R2_001.fastq.gz	fastq fastq	33350512622.0	110432161.0	GSM5737713 r1	0:151 1:151	A:8360198472;C:7386110257;G:7035347185;T:10568307654;N:549054	151	151		8360198472	7386110257	7035347185	10568307654	549054	SRX13426489	SRS11327476	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.03922	0.9568	0.00551	0.13993	0.99746	0.87986	0.74609	0.82701	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67712	67712	SRR17247460	SRX13426489	SRS11327476	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish nov2019 mcs 1	GSM5737713	source name:zebrafish kidney marrow\|Stage:adult\|class:mcs/control\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish nov2019 mcs 1	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:mcs/control\|tissue:kidney marrow	GSM5737713	GSM5737713: zfish nov2019 mcs 1; Danio rerio; RNA Seq	GSM5737713 r1	GSM5737713	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		m_1_S3_L002_R1_001.fastq.gz m_1_S3_L002_R2_001.fastq.gz	fastq fastq	33891533844.0	112223622.0	GSM5737713 r2	0:151 1:151	A:8478231309;C:7511148473;G:7106223638;T:10795407036;N:523388	151	151		8478231309	7511148473	7106223638	10795407036	523388	SRX13426489	SRS11327476	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.04314	0.95776	0.00612	0.13878	0.99748	0.88034	0.73313	0.82614	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67713	67713	SRR17247461	SRX13426488	SRS11327475	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish nov2019 cxcl8 2	GSM5737712	source name:zebrafish kidney marrow\|Stage:adult\|class:cxcl8\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish nov2019 cxcl8 2	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:cxcl8\|tissue:kidney marrow	GSM5737712	GSM5737712: zfish nov2019 cxcl8 2; Danio rerio; RNA Seq	GSM5737712 r1	GSM5737712	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		8_2_S2_L001_R1_001.fastq.gz 8_2_S2_L001_R2_001.fastq.gz	fastq fastq	33608129796.0	111285198.0	GSM5737712 r1	0:151 1:151	A:8722877609;C:6922385996;G:6668063034;T:11294249015;N:554142	151	151		8722877609	6922385996	6668063034	11294249015	554142	SRX13426488	SRS11327475	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02552	0.94052	0.0043	0.14674	0.9976	0.86466	0.72964	0.733	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67714	67714	SRR17247462	SRX13426488	SRS11327475	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish nov2019 cxcl8 2	GSM5737712	source name:zebrafish kidney marrow\|Stage:adult\|class:cxcl8\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish nov2019 cxcl8 2	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:cxcl8\|tissue:kidney marrow	GSM5737712	GSM5737712: zfish nov2019 cxcl8 2; Danio rerio; RNA Seq	GSM5737712 r1	GSM5737712	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		8_2_S2_L002_R1_001.fastq.gz 8_2_S2_L002_R2_001.fastq.gz	fastq fastq	34101912178.0	112920239.0	GSM5737712 r2	0:151 1:151	A:8834924454;C:7026706140;G:6723081178;T:11516672500;N:527906	151	151		8834924454	7026706140	6723081178	11516672500	527906	SRX13426488	SRS11327475	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02981	0.94163	0.00539	0.14603	0.99744	0.86545	0.72068	0.74612	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67715	67715	SRR17247463	SRX13426487	SRS11327474	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish nov2019 cxcl8 1	GSM5737711	source name:zebrafish kidney marrow\|Stage:adult\|class:cxcl8\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish nov2019 cxcl8 1	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:cxcl8\|tissue:kidney marrow	GSM5737711	GSM5737711: zfish nov2019 cxcl8 1; Danio rerio; RNA Seq	GSM5737711 r1	GSM5737711	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		8_1_S1_L001_R1_001.fastq.gz 8_1_S1_L001_R2_001.fastq.gz	fastq fastq	36951871984.0	122357192.0	GSM5737711 r1	0:151 1:151	A:9626031126;C:7570369217;G:7302558662;T:12452305774;N:607205	151	151		9626031126	7570369217	7302558662	12452305774	607205	SRX13426487	SRS11327474	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02737	0.93641	0.00404	0.1541	0.99736	0.85508	0.7563	0.72637	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67716	67716	SRR17247464	SRX13426487	SRS11327474	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish nov2019 cxcl8 1	GSM5737711	source name:zebrafish kidney marrow\|Stage:adult\|class:cxcl8\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish nov2019 cxcl8 1	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:cxcl8\|tissue:kidney marrow	GSM5737711	GSM5737711: zfish nov2019 cxcl8 1; Danio rerio; RNA Seq	GSM5737711 r1	GSM5737711	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		8_1_S1_L002_R1_001.fastq.gz 8_1_S1_L002_R2_001.fastq.gz	fastq fastq	37469129128.0	124069964.0	GSM5737711 r2	0:151 1:151	A:9743940391;C:7679263985;G:7358502754;T:12686838441;N:583557	151	151		9743940391	7679263985	7358502754	12686838441	583557	SRX13426487	SRS11327474	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02963	0.93729	0.00529	0.15304	0.99734	0.85492	0.71942	0.71806	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67717	67717	SRR17247465	SRX13426486	SRS11327472	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish km july2020 prkcda 2 gex	GSM5737710	source name:zebrafish kidney marrow\|Stage:adult\|class:prkcda\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish km july2020 prkcda 2 gex	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:prkcda\|tissue:kidney marrow	GSM5737710	GSM5737710: zfish km july2020 prkcda 2 gex; Danio rerio; RNA Seq	GSM5737710 r1	GSM5737710	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		prkcda_2_gex_S2_L001_R1_001.fastq.gz prkcda_2_gex_S2_L001_R2_001.fastq.gz	fastq fastq	13835729850.0	45813675.0	GSM5737710 r1	0:151 1:151	A:3702098746;C:2530292707;G:2281467337;T:5321602811;N:268249	151	151		3702098746	2530292707	2281467337	5321602811	268249	SRX13426486	SRS11327472	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02335	0.84758	0.00679	0.11459	0.99159	0.81793	0.56734	0.57225	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67718	67718	SRR17247466	SRX13426486	SRS11327472	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish km july2020 prkcda 2 gex	GSM5737710	source name:zebrafish kidney marrow\|Stage:adult\|class:prkcda\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish km july2020 prkcda 2 gex	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:prkcda\|tissue:kidney marrow	GSM5737710	GSM5737710: zfish km july2020 prkcda 2 gex; Danio rerio; RNA Seq	GSM5737710 r1	GSM5737710	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		prkcda_2_gex_S2_L002_R1_001.fastq.gz prkcda_2_gex_S2_L002_R2_001.fastq.gz	fastq fastq	12732723472.0	42161336.0	GSM5737710 r2	0:151 1:151	A:3401432115;C:2329599383;G:2131111574;T:4870319578;N:260822	151	151		3401432115	2329599383	2131111574	4870319578	260822	SRX13426486	SRS11327472	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.01889	0.8502	0.00458	0.11409	0.99239	0.81708	0.56652	0.5669	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67719	67719	SRR17247467	SRX13426485	SRS11327473	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish km july2020 prkcda 1 gex	GSM5737709	source name:zebrafish kidney marrow\|Stage:adult\|class:prkcda\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish km july2020 prkcda 1 gex	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:prkcda\|tissue:kidney marrow	GSM5737709	GSM5737709: zfish km july2020 prkcda 1 gex; Danio rerio; RNA Seq	GSM5737709 r1	GSM5737709	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		prkcda_1_gex_S1_L001_R1_001.fastq.gz prkcda_1_gex_S1_L001_R2_001.fastq.gz	fastq fastq	14142779894.0	46830397.0	GSM5737709 r1	0:151 1:151	A:3803907364;C:2547631786;G:2315347877;T:5475620885;N:271982	151	151		3803907364	2547631786	2315347877	5475620885	271982	SRX13426485	SRS11327473	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02414	0.84338	0.00622	0.11548	0.99097	0.8144	0.62514	0.57188	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67720	67720	SRR17247468	SRX13426485	SRS11327473	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish km july2020 prkcda 1 gex	GSM5737709	source name:zebrafish kidney marrow\|Stage:adult\|class:prkcda\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish km july2020 prkcda 1 gex	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:prkcda\|tissue:kidney marrow	GSM5737709	GSM5737709: zfish km july2020 prkcda 1 gex; Danio rerio; RNA Seq	GSM5737709 r1	GSM5737709	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		prkcda_1_gex_S1_L002_R1_001.fastq.gz prkcda_1_gex_S1_L002_R2_001.fastq.gz	fastq fastq	13035917882.0	43165291.0	GSM5737709 r2	0:151 1:151	A:3500572922;C:2349111864;G:2165763483;T:5020201575;N:268038	151	151		3500572922	2349111864	2165763483	5020201575	268038	SRX13426485	SRS11327473	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02024	0.84227	0.00588	0.1153	0.99289	0.81746	0.60227	0.56302	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67721	67721	SRR17247469	SRX13426484	SRS11327471	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish km july2020 mcs 2 gex	GSM5737708	source name:zebrafish kidney marrow\|Stage:adult\|class:mcs/control\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish km july2020 mcs 2 gex	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:mcs/control\|tissue:kidney marrow	GSM5737708	GSM5737708: zfish km july2020 mcs 2 gex; Danio rerio; RNA Seq	GSM5737708 r1	GSM5737708	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		mcs_2_gex_S4_L001_R1_001.fastq.gz mcs_2_gex_S4_L001_R2_001.fastq.gz	fastq fastq	16896987882.0	55950291.0	GSM5737708 r1	0:151 1:151	A:4591971940;C:3075167390;G:2821138917;T:6408383413;N:326222	151	151		4591971940	3075167390	2821138917	6408383413	326222	SRX13426484	SRS11327471	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02543	0.89539	0.00682	0.1299	0.99019	0.79162	0.58431	0.57222	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67722	67722	SRR17247470	SRX13426484	SRS11327471	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish km july2020 mcs 2 gex	GSM5737708	source name:zebrafish kidney marrow\|Stage:adult\|class:mcs/control\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish km july2020 mcs 2 gex	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:mcs/control\|tissue:kidney marrow	GSM5737708	GSM5737708: zfish km july2020 mcs 2 gex; Danio rerio; RNA Seq	GSM5737708 r1	GSM5737708	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		mcs_2_gex_S4_L002_R1_001.fastq.gz mcs_2_gex_S4_L002_R2_001.fastq.gz	fastq fastq	15528315124.0	51418262.0	GSM5737708 r2	0:151 1:151	A:4211257903;C:2827053832;G:2631217951;T:5858464915;N:320523	151	151		4211257903	2827053832	2631217951	5858464915	320523	SRX13426484	SRS11327471	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02206	0.89665	0.00561	0.13079	0.99149	0.79178	0.59462	0.56762	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67723	67723	SRR17247471	SRX13426483	SRS11327470	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish km july2020 mcs 1 gex	GSM5737707	source name:zebrafish kidney marrow\|Stage:adult\|class:mcs/control\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish km july2020 mcs 1 gex	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:mcs/control\|tissue:kidney marrow	GSM5737707	GSM5737707: zfish km july2020 mcs 1 gex; Danio rerio; RNA Seq	GSM5737707 r1	GSM5737707	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		mcs_1_gex_S3_L001_R1_001.fastq.gz mcs_1_gex_S3_L001_R2_001.fastq.gz	fastq fastq	20942692528.0	69346664.0	GSM5737707 r1	0:151 1:151	A:5740347455;C:3760947039;G:3428436604;T:8012559458;N:401972	151	151		5740347455	3760947039	3428436604	8012559458	401972	SRX13426483	SRS11327470	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02601	0.88017	0.00646	0.1351	0.98959	0.79711	0.62833	0.56309	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
67724	67724	SRR17247472	SRX13426483	SRS11327470	SRP351089	PRJNA789478	Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C	GSE191029	Other	Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.		pubmed:37209097	zfish km july2020 mcs 1 gex	GSM5737707	source name:zebrafish kidney marrow\|Stage:adult\|class:mcs/control\|tissue:kidney marrow\|geo loc name:missing\|collection date:missing	zfish km july2020 mcs 1 gex	scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.	zebrafish kidney marrow	No treatments	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.	Fish were maintained on a recirculating water system at 28C.	Stage:adult\|class:mcs/control\|tissue:kidney marrow	GSM5737707	GSM5737707: zfish km july2020 mcs 1 gex; Danio rerio; RNA Seq	GSM5737707 r1	GSM5737707	1	Fish were euthanized and kidney marrow was dissected RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351089		mcs_1_gex_S3_L002_R1_001.fastq.gz mcs_1_gex_S3_L002_R2_001.fastq.gz	fastq fastq	19312854398.0	63949849.0	GSM5737707 r2	0:151 1:151	A:5284897528;C:3469277015;G:3207797556;T:7350475426;N:406873	151	151		5284897528	3469277015	3207797556	7350475426	406873	SRX13426483	SRS11327470	SRA1347311	Blaser Lab, Comprehensive Cancer Center, Ohio State University	Blaser Lab, Comprehensive Cancer Center, Ohio State University	2	0.02195	0.88364	0.00566	0.1347	0.99127	0.79799	0.63511	0.57074	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-16	Adult	Adult	Kidney	Renal System
72561	72561	SRR22722190	SRX18683720	SRS16126888	SRP412911	PRJNA911847	Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia	PRJNA911847	Other	Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening				Transgenic FLT3 ITD IDH2 R140Q	strain:TU\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:8 month\|dev stage:8 month\|sex:pooled male and female\|tissue:kidney marrow\|genotype:Transgenic Runx1:FLT3ITDIDH2R140Q\|BioSampleModel:Model organism or animal									Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R140Q	ITD140Q	ITD140Q	Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.			OTHER	TRANSCRIPTOMIC	other	PAIRED	DNBSEQ	DNBSEQ-G400	SRP412911	loader:fastq load.py	ITD172KA_S1_L001_I1_001.fastq.gz ITD172KA_S1_L001_R1_001.fastq.gz ITD172KA_S1_L001_R2_001.fastq.gz	fastq fastq fastq	52149830422.0	410628586.0	ITD172KA S1 L001 I1 001.fastq.gz	0:8 1:28 2:91	A:10282953217;C:8459559201;G:8851285287;T:9772343870;N:1059751	8	28	91	10282953217	8459559201	8851285287	9772343870	1059751	SRX18683720	SRS16126888	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.88465		0.13112		0.81789		0.55842		91		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2022-12-14	Adult	Adult	Kidney	Renal System
72562	72562	SRR22722191	SRX18683719	SRS16126887	SRP412911	PRJNA911847	Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia	PRJNA911847	Other	Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening				Transgenic FLT3 ITD IDH2 R172K	strain:TU\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:8 month\|dev stage:8 month\|sex:pooled male and female\|tissue:kidney marrow\|genotype:Transgenic Runx1:FLT3ITDIDH2R172K\|BioSampleModel:Model organism or animal									Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R172K	ITD172K	ITD172K	Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.			OTHER	TRANSCRIPTOMIC	other	PAIRED	DNBSEQ	DNBSEQ-G400	SRP412911	loader:fastq load.py	ITD140QA_S1_L004_I1_001.fastq.gz ITD140QA_S1_L004_R1_001.fastq.gz ITD140QA_S1_L004_R2_001.fastq.gz	fastq fastq fastq	28595025233.0	225157679.0	ITD140QA S1 L004 I1 001.fastq.gz	0:8 1:28 2:91	A:5628987577;C:4565848641;G:4959209904;T:5302394659;N:32908008	8	28	91	5628987577	4565848641	4959209904	5302394659	32908008	SRX18683719	SRS16126887	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.81404		0.11315		0.83327		0.56222		91		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2022-12-13	Adult	Adult	Kidney	Renal System
72563	72563	SRR22722192	SRX18683718	SRS16126886	SRP412911	PRJNA911847	Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia	PRJNA911847	Other	Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening				Wild type	strain:TU\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:8 month\|dev stage:8 month\|sex:pooled male and female\|tissue:kidney marrow\|genotype:Wild type\|BioSampleModel:Model organism or animal									Single cell RNA seq of Danio rerio: Wild type	Control	Control	Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.			OTHER	TRANSCRIPTOMIC	other	PAIRED	DNBSEQ	DNBSEQ-G400	SRP412911	loader:fastq load.py	ControlA_S1_L003_R2_001.fastq.gz ControlA_S1_L003_R1_001.fastq.gz ControlA_S1_L003_I1_001.fastq.gz	fastq fastq fastq	37892727491.0	298367933.0	ControlA S1 L003 I1 001.fastq.gz	0:8 1:28 2:91	A:7386602298;C:6174680460;G:6579652828;T:6955791213;N:54755104	8	28	91	7386602298	6174680460	6579652828	6955791213	54755104	SRX18683718	SRS16126886	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.81686		0.11049		0.84139		0.46084		91		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2022-12-14	Adult	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");;