metadata: run_metadata: 16 rows where experiment.library_layout = "PAIRED", technology = "10x" and tissue

16 rows where experiment.library_layout = "PAIRED", technology = "10x" and tissue_curation = "Marrow"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
69438	69438	SRR18687231	SRX14788266	SRS12547158	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	Mutant 5mpf scRNAseq	GSM6035264	source name:wkm\|tissue:marrow\|age:5mpf\|genotype:gata2a /	Mutant 5mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:5mpf\|genotype:gata2a /	GSM6035264	GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq	GSM6035264 r1	GSM6035264	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	MUTANT_S2_L001_I1_001.fastq.gz MUTANT_S2_L001_R1_001.fastq.gz MUTANT_S2_L001_R2_001.fastq.gz	fastq fastq fastq	7173831982.0	56486866.0	GSM6035264 r1	0:8 1:28 2:91	A:1358934535;C:1244254049;G:1282298109;T:1250397550;N:4420563	8	28	91	1358934535	1244254049	1282298109	1250397550	4420563	SRX14788266	SRS12547158	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.96273	0.07511	0.84861	0.53711	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69439	69439	SRR18687232	SRX14788266	SRS12547158	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	Mutant 5mpf scRNAseq	GSM6035264	source name:wkm\|tissue:marrow\|age:5mpf\|genotype:gata2a /	Mutant 5mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:5mpf\|genotype:gata2a /	GSM6035264	GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq	GSM6035264 r1	GSM6035264	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	MUTANT_S2_L002_I1_001.fastq.gz MUTANT_S2_L002_R1_001.fastq.gz MUTANT_S2_L002_R2_001.fastq.gz	fastq fastq fastq	7052205352.0	55529176.0	GSM6035264 r2	0:8 1:28 2:91	A:1335427840;C:1223120616;G:1262490348;T:1228023814;N:4092398	8	28	91	1335427840	1223120616	1262490348	1228023814	4092398	SRX14788266	SRS12547158	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.96332	0.07559	0.84869	0.53571	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69440	69440	SRR18687233	SRX14788266	SRS12547158	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	Mutant 5mpf scRNAseq	GSM6035264	source name:wkm\|tissue:marrow\|age:5mpf\|genotype:gata2a /	Mutant 5mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:5mpf\|genotype:gata2a /	GSM6035264	GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq	GSM6035264 r1	GSM6035264	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	MUTANT_S2_L003_I1_001.fastq.gz MUTANT_S2_L003_R1_001.fastq.gz MUTANT_S2_L003_R2_001.fastq.gz	fastq fastq fastq	7121271889.0	56073007.0	GSM6035264 r3	0:8 1:28 2:91	A:1348956241;C:1235761797;G:1273552429;T:1240317702;N:4055468	8	28	91	1348956241	1235761797	1273552429	1240317702	4055468	SRX14788266	SRS12547158	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.96323	0.07544	0.84776	0.54532	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69441	69441	SRR18687234	SRX14788266	SRS12547158	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	Mutant 5mpf scRNAseq	GSM6035264	source name:wkm\|tissue:marrow\|age:5mpf\|genotype:gata2a /	Mutant 5mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:5mpf\|genotype:gata2a /	GSM6035264	GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq	GSM6035264 r1	GSM6035264	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	MUTANT_S2_L004_I1_001.fastq.gz MUTANT_S2_L004_R1_001.fastq.gz MUTANT_S2_L004_R2_001.fastq.gz	fastq fastq fastq	7060634088.0	55595544.0	GSM6035264 r4	0:8 1:28 2:91	A:1337923427;C:1225128065;G:1262793134;T:1229767092;N:3582786	8	28	91	1337923427	1225128065	1262793134	1229767092	3582786	SRX14788266	SRS12547158	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.96323	0.07552	0.84626	0.53808	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69442	69442	SRR18687235	SRX14788265	SRS12547159	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	WT 5mpf scRNA seq	GSM6035263	source name:wkm\|tissue:marrow\|age:5mpf\|genotype:WT	WT 5mpf scRNA seq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:5mpf\|genotype:WT	GSM6035263	GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq	GSM6035263 r1	GSM6035263	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	WT_S1_L001_I1_001.fastq.gz WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz	fastq fastq fastq	7887658469.0	62107547.0	GSM6035263 r1	0:8 1:28 2:91	A:1686084589;C:1207047546;G:1347307215;T:1406353747;N:4993680	8	28	91	1686084589	1207047546	1347307215	1406353747	4993680	SRX14788265	SRS12547159	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.93208	0.13464	0.82885	0.5507	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69443	69443	SRR18687236	SRX14788265	SRS12547159	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	WT 5mpf scRNA seq	GSM6035263	source name:wkm\|tissue:marrow\|age:5mpf\|genotype:WT	WT 5mpf scRNA seq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:5mpf\|genotype:WT	GSM6035263	GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq	GSM6035263 r1	GSM6035263	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	WT_S1_L002_I1_001.fastq.gz WT_S1_L002_R1_001.fastq.gz WT_S1_L002_R2_001.fastq.gz	fastq fastq fastq	7726846751.0	60841313.0	GSM6035263 r2	0:8 1:28 2:91	A:1651285269;C:1182541074;G:1321442374;T:1376689852;N:4600914	8	28	91	1651285269	1182541074	1321442374	1376689852	4600914	SRX14788265	SRS12547159	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.93139	0.13512	0.83157	0.54659	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69444	69444	SRR18687237	SRX14788265	SRS12547159	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	WT 5mpf scRNA seq	GSM6035263	source name:wkm\|tissue:marrow\|age:5mpf\|genotype:WT	WT 5mpf scRNA seq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:5mpf\|genotype:WT	GSM6035263	GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq	GSM6035263 r1	GSM6035263	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	WT_S1_L003_I1_001.fastq.gz WT_S1_L003_R1_001.fastq.gz WT_S1_L003_R2_001.fastq.gz	fastq fastq fastq	7809746382.0	61494066.0	GSM6035263 r3	0:8 1:28 2:91	A:1669649704;C:1195820935;G:1334457445;T:1391506607;N:4525315	8	28	91	1669649704	1195820935	1334457445	1391506607	4525315	SRX14788265	SRS12547159	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.9319	0.13521	0.83039	0.54131	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69445	69445	SRR18687238	SRX14788265	SRS12547159	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	WT 5mpf scRNA seq	GSM6035263	source name:wkm\|tissue:marrow\|age:5mpf\|genotype:WT	WT 5mpf scRNA seq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:5mpf\|genotype:WT	GSM6035263	GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq	GSM6035263 r1	GSM6035263	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	WT_S1_L004_I1_001.fastq.gz WT_S1_L004_R1_001.fastq.gz WT_S1_L004_R2_001.fastq.gz	fastq fastq fastq	7741554113.0	60957119.0	GSM6035263 r4	0:8 1:28 2:91	A:1655590157;C:1185244017;G:1323146581;T:1379127206;N:3989868	8	28	91	1655590157	1185244017	1323146581	1379127206	3989868	SRX14788265	SRS12547159	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.93299	0.13493	0.82852	0.55166	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69446	69446	SRR18687240	SRX14788264	SRS12547155	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	Mutant 12mpf scRNAseq	GSM6035262	source name:wkm\|tissue:marrow\|age:12mpf\|genotype:gata2a /	Mutant 12mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:12mpf\|genotype:gata2a /	GSM6035262	GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq	GSM6035262 r1	GSM6035262	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	mutant_S2_L001_I1_001.fastq.gz mutant_S2_L001_R1_001.fastq.gz mutant_S2_L001_R2_001.fastq.gz	fastq fastq fastq	2802332148.0	21229789.0	GSM6035262 r1	0:8 1:26 2:98	A:640368763;C:436216313;G:577751307;T:426047488;N:135451	8	26	98	640368763	436216313	577751307	426047488	135451	SRX14788264	SRS12547155	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.95554	0.01147	0.92565	0.57239	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69447	69447	SRR18687241	SRX14788264	SRS12547155	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	Mutant 12mpf scRNAseq	GSM6035262	source name:wkm\|tissue:marrow\|age:12mpf\|genotype:gata2a /	Mutant 12mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:12mpf\|genotype:gata2a /	GSM6035262	GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq	GSM6035262 r1	GSM6035262	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	mutant_S2_L002_I1_001.fastq.gz mutant_S2_L002_R1_001.fastq.gz mutant_S2_L002_R2_001.fastq.gz	fastq fastq fastq	2716435392.0	20579056.0	GSM6035262 r2	0:8 1:26 2:98	A:630665836;C:423337212;G:549434401;T:413134647;N:175392	8	26	98	630665836	423337212	549434401	413134647	175392	SRX14788264	SRS12547155	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.95616	0.01121	0.92638	0.59372	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69448	69448	SRR18687242	SRX14788264	SRS12547155	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	Mutant 12mpf scRNAseq	GSM6035262	source name:wkm\|tissue:marrow\|age:12mpf\|genotype:gata2a /	Mutant 12mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:12mpf\|genotype:gata2a /	GSM6035262	GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq	GSM6035262 r1	GSM6035262	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	mutant_S2_L003_I1_001.fastq.gz mutant_S2_L003_R1_001.fastq.gz mutant_S2_L003_R2_001.fastq.gz	fastq fastq fastq	2866261860.0	21714105.0	GSM6035262 r3	0:8 1:26 2:98	A:662138328;C:448896468;G:581624031;T:434958720;N:364743	8	26	98	662138328	448896468	581624031	434958720	364743	SRX14788264	SRS12547155	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.95475	0.0112	0.9264	0.57664	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69449	69449	SRR18687243	SRX14788264	SRS12547155	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	Mutant 12mpf scRNAseq	GSM6035262	source name:wkm\|tissue:marrow\|age:12mpf\|genotype:gata2a /	Mutant 12mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:12mpf\|genotype:gata2a /	GSM6035262	GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq	GSM6035262 r1	GSM6035262	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	mutant_S2_L004_I1_001.fastq.gz mutant_S2_L004_R1_001.fastq.gz mutant_S2_L004_R2_001.fastq.gz	fastq fastq fastq	2778700584.0	21050762.0	GSM6035262 r4	0:8 1:26 2:98	A:646107299;C:435138523;G:558295882;T:423168974;N:263998	8	26	98	646107299	435138523	558295882	423168974	263998	SRX14788264	SRS12547155	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.95523	0.01148	0.92612	0.594	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69450	69450	SRR18687249	SRX14788262	SRS12547153	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	WT 12mpf scRNAseq	GSM6035261	source name:wkm\|tissue:marrow\|age:12mpf\|genotype:WT	WT 12mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:12mpf\|genotype:WT	GSM6035261	GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq	GSM6035261 r1	GSM6035261	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	WT-12mpf_S1_L001_I1_001.fastq.gz WT-12mpf_S1_L001_R1_001.fastq.gz WT-12mpf_S1_L001_R2_001.fastq.gz	fastq fastq fastq	2871526284.0	21753987.0	GSM6035261 r1	0:8 1:26 2:98	A:657935861;C:458782361;G:577643976;T:437389248;N:139280	8	26	98	657935861	458782361	577643976	437389248	139280	SRX14788262	SRS12547153	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.95618	0.01409	0.93137	0.57474	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69451	69451	SRR18687250	SRX14788262	SRS12547153	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	WT 12mpf scRNAseq	GSM6035261	source name:wkm\|tissue:marrow\|age:12mpf\|genotype:WT	WT 12mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:12mpf\|genotype:WT	GSM6035261	GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq	GSM6035261 r1	GSM6035261	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	WT-12mpf_S1_L002_I1_001.fastq.gz WT-12mpf_S1_L002_R1_001.fastq.gz WT-12mpf_S1_L002_R2_001.fastq.gz	fastq fastq fastq	2786830992.0	21112356.0	GSM6035261 r2	0:8 1:26 2:98	A:646477118;C:445716938;G:552088162;T:424546694;N:181976	8	26	98	646477118	445716938	552088162	424546694	181976	SRX14788262	SRS12547153	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.95703	0.01387	0.93117	0.57965	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69452	69452	SRR18687251	SRX14788262	SRS12547153	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	WT 12mpf scRNAseq	GSM6035261	source name:wkm\|tissue:marrow\|age:12mpf\|genotype:WT	WT 12mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:12mpf\|genotype:WT	GSM6035261	GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq	GSM6035261 r1	GSM6035261	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	WT-12mpf_S1_L003_I1_001.fastq.gz WT-12mpf_S1_L003_R1_001.fastq.gz WT-12mpf_S1_L003_R2_001.fastq.gz	fastq fastq fastq	2940233472.0	22274496.0	GSM6035261 r3	0:8 1:26 2:98	A:678078355;C:472082276;G:585591377;T:446774858;N:373742	8	26	98	678078355	472082276	585591377	446774858	373742	SRX14788262	SRS12547153	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.95649	0.01398	0.93237	0.5686	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	Renal System
69453	69453	SRR18687252	SRX14788262	SRS12547153	SRP368307	PRJNA824844	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals	GSE200503	Other	Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability	WT 12mpf scRNAseq	GSM6035261	source name:wkm\|tissue:marrow\|age:12mpf\|genotype:WT	WT 12mpf scRNAseq	scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11	wkm	cells were not treated	10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf	tissue:marrow\|age:12mpf\|genotype:WT	GSM6035261	GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq	GSM6035261 r1	GSM6035261	1	10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP368307	loader:fastq load.py	WT-12mpf_S1_L004_I1_001.fastq.gz WT-12mpf_S1_L004_R1_001.fastq.gz WT-12mpf_S1_L004_R2_001.fastq.gz	fastq fastq fastq	2850270720.0	21592960.0	GSM6035261 r4	0:8 1:26 2:98	A:661215163;C:457617537;G:562445244;T:434561966;N:270170	8	26	98	661215163	457617537	562445244	434561966	270170	SRX14788262	SRS12547153	SRA1400926	Institute of Cancer and Genomic Sciences, University of Birminhgam	Institute of Cancer and Genomic Sciences, University of Birminhgam	1	0.952	0.0139	0.93188	0.56069	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2022-04-08	Adult	Adult	Marrow	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");;