metadata: run_metadata: 17 rows where experiment.library_selection = "RANDOM", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "10x"

17 rows where experiment.library_selection = "RANDOM", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "10x"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	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.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.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
15614	15614	ERR13109732	ERX12481366	ERS19896183	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	WT young	SAMEA115618603	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:WT young\|age:12\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bWT\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:WT young\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed WT	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:WT young p	WT young p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	WT_young_S16_L002_I1_001.fastq.gz WT_young_S16_L002_R1_001.fastq.gz WT_young_S16_L002_R2_001.fastq.gz	fastq fastq fastq	11547230144.0	90923072.0	E MTAB 14075:WT young S16 L002	0:8 1:28 2:91	A:2298760158;C:1887715706;G:1977278606;T:2109839457;N:405625	8	28	91	2298760158	1887715706	1977278606	2109839457	405625	ERX12481366	ERS19896183	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15615	15615	ERR13109737	ERX12481366	ERS19896183	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	WT young	SAMEA115618603	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:WT young\|age:12\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bWT\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:WT young\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed WT	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:WT young p	WT young p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	WT_young_run2_S10_L001_I1_001.fastq.gz WT_young_run2_S10_L001_R1_001.fastq.gz WT_young_run2_S10_L001_R2_001.fastq.gz	fastq fastq fastq	6300899375.0	50407195.0	E MTAB 14075:WT young run2 S10 L001	0:8 1:28 2:89	A:1243074350;C:1030040216;G:1079454879;T:1133663108;N:7802	8	28	89	1243074350	1030040216	1079454879	1133663108	7802	ERX12481366	ERS19896183	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15616	15616	ERR13109733	ERX12481366	ERS19896183	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	WT young	SAMEA115618603	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:WT young\|age:12\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bWT\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:WT young\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed WT	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:WT young p	WT young p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	WT_young_run2_S10_L002_I1_001.fastq.gz WT_young_run2_S10_L002_R1_001.fastq.gz WT_young_run2_S10_L002_R2_001.fastq.gz	fastq fastq fastq	6323980500.0	50591844.0	E MTAB 14075:WT young run2 S10 L002	0:8 1:28 2:89	A:1248024810;C:1032976792;G:1082805513;T:1138855823;N:11178	8	28	89	1248024810	1032976792	1082805513	1138855823	11178	ERX12481366	ERS19896183	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15617	15617	ERR13109728	ERX12481366	ERS19896183	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	WT young	SAMEA115618603	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:WT young\|age:12\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bWT\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:WT young\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed WT	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:WT young p	WT young p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	WT_young_S16_L001_I1_001.fastq.gz WT_young_S16_L001_R1_001.fastq.gz WT_young_S16_L001_R2_001.fastq.gz	fastq fastq fastq	9395132467.0	73977421.0	E MTAB 14075:WT young S16 L001	0:8 1:28 2:91	A:1870197969;C:1535772308;G:1609450193;T:1716224344;N:300497	8	28	91	1870197969	1535772308	1609450193	1716224344	300497	ERX12481366	ERS19896183	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15618	15618	ERR13109727	ERX12481365	ERS19896182	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	WT aged	SAMEA115618602	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:WT aged\|age:18\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bWT\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:WT aged\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed WT	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:WT aged p	WT aged p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	WT_aged_S15_L001_I1_001.fastq.gz WT_aged_S15_L001_R1_001.fastq.gz WT_aged_S15_L001_R2_001.fastq.gz	fastq fastq fastq	3224055528.0	25386264.0	E MTAB 14075:WT aged S15 L001	0:8 1:28 2:91	A:632762441;C:548488749;G:552881879;T:575917355;N:99600	8	28	91	632762441	548488749	552881879	575917355	99600	ERX12481365	ERS19896182	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15619	15619	ERR13109729	ERX12481365	ERS19896182	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	WT aged	SAMEA115618602	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:WT aged\|age:18\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bWT\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:WT aged\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed WT	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:WT aged p	WT aged p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	WT_aged_S15_L002_I1_001.fastq.gz WT_aged_S15_L002_R1_001.fastq.gz WT_aged_S15_L002_R2_001.fastq.gz	fastq fastq fastq	4178136043.0	32898709.0	E MTAB 14075:WT aged S15 L002	0:8 1:28 2:91	A:820476445;C:710661272;G:715891121;T:746611018;N:142663	8	28	91	820476445	710661272	715891121	746611018	142663	ERX12481365	ERS19896182	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15620	15620	ERR13109731	ERX12481365	ERS19896182	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	WT aged	SAMEA115618602	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:WT aged\|age:18\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bWT\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:WT aged\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed WT	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:WT aged p	WT aged p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	WT_aged_run2_S13_L002_I1_001.fastq.gz WT_aged_run2_S13_L002_R1_001.fastq.gz WT_aged_run2_S13_L002_R2_001.fastq.gz	fastq fastq fastq	11315635500.0	90525084.0	E MTAB 14075:WT aged run2 S13 L002	0:8 1:28 2:89	A:2205965370;C:1918372621;G:1938090305;T:1994285205;N:18975	8	28	89	2205965370	1918372621	1938090305	1994285205	18975	ERX12481365	ERS19896182	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15621	15621	ERR13109734	ERX12481365	ERS19896182	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	WT aged	SAMEA115618602	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:WT aged\|age:18\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bWT\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:WT aged\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed WT	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:WT aged p	WT aged p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	WT_aged_run2_S13_L001_I1_001.fastq.gz WT_aged_run2_S13_L001_R1_001.fastq.gz WT_aged_run2_S13_L001_R2_001.fastq.gz	fastq fastq fastq	11297009750.0	90376078.0	E MTAB 14075:WT aged run2 S13 L001	0:8 1:28 2:89	A:2201626807;C:1916371507;G:1936001373;T:1989457619;N:13636	8	28	89	2201626807	1916371507	1936001373	1989457619	13636	ERX12481365	ERS19896182	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15622	15622	ERR13109730	ERX12481363	ERS19896180	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	Het aged	SAMEA115618600	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:Het aged\|age:18\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bHet\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:Het aged\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed Gata2b KO	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:Het aged p	Het aged p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Het_aged_run2_S14_L002_I1_001.fastq.gz Het_aged_run2_S14_L002_R1_001.fastq.gz Het_aged_run2_S14_L002_R2_001.fastq.gz	fastq fastq fastq	4755473375.0	38043787.0	E MTAB 14075:Het aged run2 S14 L002	0:8 1:28 2:89	A:924628155;C:804435427;G:826904786;T:829920091;N:8584	8	28	89	924628155	804435427	826904786	829920091	8584	ERX12481363	ERS19896180	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15623	15623	ERR13109738	ERX12481363	ERS19896180	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	Het aged	SAMEA115618600	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:Het aged\|age:18\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bHet\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:Het aged\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed Gata2b KO	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:Het aged p	Het aged p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Het_aged_run2_S14_L001_I1_001.fastq.gz Het_aged_run2_S14_L001_R1_001.fastq.gz Het_aged_run2_S14_L001_R2_001.fastq.gz	fastq fastq fastq	4757077375.0	38056619.0	E MTAB 14075:Het aged run2 S14 L001	0:8 1:28 2:89	A:924804478;C:805146986;G:827570549;T:829511132;N:5946	8	28	89	924804478	805146986	827570549	829511132	5946	ERX12481363	ERS19896180	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15624	15624	ERR13109725	ERX12481363	ERS19896180	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	Het aged	SAMEA115618600	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:Het aged\|age:18\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bHet\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:Het aged\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed Gata2b KO	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:Het aged p	Het aged p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Het_aged_S13_L001_I1_001.fastq.gz Het_aged_S13_L001_R1_001.fastq.gz Het_aged_S13_L001_R2_001.fastq.gz	fastq fastq fastq	2031302643.0	15994509.0	E MTAB 14075:Het aged S13 L001	0:8 1:28 2:91	A:398278357;C:344264985;G:353424298;T:359473296;N:59383	8	28	91	398278357	344264985	353424298	359473296	59383	ERX12481363	ERS19896180	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15625	15625	ERR13109739	ERX12481363	ERS19896180	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	Het aged	SAMEA115618600	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:Het aged\|age:18\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bHet\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:Het aged\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed Gata2b KO	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:Het aged p	Het aged p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Het_aged_S13_L002_I1_001.fastq.gz Het_aged_S13_L002_R1_001.fastq.gz Het_aged_S13_L002_R2_001.fastq.gz	fastq fastq fastq	2430576292.0	19138396.0	E MTAB 14075:Het aged S13 L002	0:8 1:28 2:91	A:476457271;C:411953563;G:422659830;T:430445714;N:77658	8	28	91	476457271	411953563	422659830	430445714	77658	ERX12481363	ERS19896180	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15626	15626	ERR13109736	ERX12481364	ERS19896181	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	Het young	SAMEA115618601	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:Het young\|age:12\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bHet\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:Het young\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed Gata2b KO	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:Het young p	Het young p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Het_young_S14_L001_I1_001.fastq.gz Het_young_S14_L001_R1_001.fastq.gz Het_young_S14_L001_R2_001.fastq.gz	fastq fastq fastq	7202197051.0	56710213.0	E MTAB 14075:Het young S14 L001	0:8 1:28 2:91	A:1452033851;C:1164601809;G:1229900451;T:1313862644;N:230628	8	28	91	1452033851	1164601809	1229900451	1313862644	230628	ERX12481364	ERS19896181	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15627	15627	ERR13109740	ERX12481364	ERS19896181	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	Het young	SAMEA115618601	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:Het young\|age:12\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bHet\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:Het young\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed Gata2b KO	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:Het young p	Het young p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Het_young_run2_S11_L001_I1_001.fastq.gz Het_young_run2_S11_L001_R1_001.fastq.gz Het_young_run2_S11_L001_R2_001.fastq.gz	fastq fastq fastq	3012722750.0	24101782.0	E MTAB 14075:Het young run2 S11 L001	0:8 1:28 2:89	A:601664996;C:487380557;G:514748426;T:541261211;N:3408	8	28	89	601664996	487380557	514748426	541261211	3408	ERX12481364	ERS19896181	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15628	15628	ERR13109735	ERX12481364	ERS19896181	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	Het young	SAMEA115618601	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:Het young\|age:12\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bHet\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:Het young\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed Gata2b KO	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:Het young p	Het young p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Het_young_run2_S11_L002_I1_001.fastq.gz Het_young_run2_S11_L002_R1_001.fastq.gz Het_young_run2_S11_L002_R2_001.fastq.gz	fastq fastq fastq	3017568125.0	24140545.0	E MTAB 14075:Het young run2 S11 L002	0:8 1:28 2:89	A:602793366;C:487819335;G:515271935;T:542618728;N:5141	8	28	89	602793366	487819335	515271935	542618728	5141	ERX12481364	ERS19896181	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
15629	15629	ERR13109726	ERX12481364	ERS19896181	ERP160330	PRJEB75769	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E-MTAB-14075	Transcriptome Analysis	The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	Het young	SAMEA115618601	Department of Hematology cancer institute ErasmusMC	ENA first public:2024 11 05\|INSDC center name:Department of Hematology cancer institute ErasmusMC\|INSDC status:public\|Submitter Id:E MTAB 14075:Het young\|age:12\|broker name:ArrayExpress\|cell type:hematopoietic cell\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Gata2bHet\|geographic location country and/or sea:not collected\|individual:pools of 2 fish\|isolate:not applicable\|organism part:kidney marrow\|sample name:E MTAB 14075:Het young\|scientific name:Danio rerio\|sex:mixed\|strain:TgCD41:GFP; runx1:DsRed Gata2b KO	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	E MTAB 14075:Het young p	Het young p	Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP160330	Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish	ENA FIRST PUBLIC:2024 11 05\|ENA LAST UPDATE:2024 11 05	Het_young_S14_L002_I1_001.fastq.gz Het_young_S14_L002_R1_001.fastq.gz Het_young_S14_L002_R2_001.fastq.gz	fastq fastq fastq	8707482077.0	68562851.0	E MTAB 14075:Het young S14 L002	0:8 1:28 2:91	A:1755361511;C:1408255848;G:1486295783;T:1588996810;N:309489	8	28	91	1755361511	1408255848	1486295783	1588996810	309489	ERX12481364	ERS19896181	ERA30396266	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive							B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United Kingdom	2024-11-05	Adult	Adult	Multi-tissue	Multi-system
53593	53593	SRR11886700	SRX8434172	SRS6745285	SRP265421	PRJNA559885	A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration	PRJNA559885	Other	The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic developmental cellular and molecular studies the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio we uncovered species specific and evolutionarily conserved genomic responses to amputation.			zebrafish fin regeneration	zebrafish fin 1dpa		strain:AB\|isolate:12\|breed:N/A\|cultivar:N/A\|ecotype:N/A\|age:6 mpf\|dev stage:Adult\|sex:not collected\|tissue:caudal fin\|BioSampleModel:Model organism or animal	zebrafish blastema single cell	L41598	L41598	The African killifish and zebrafish single cell RNA seq were done with the 10x Chromium platform. About 20 fish were used for cell dissociation in each experiment. Hoechst stained cells 100 000 cells from the dissected blastema tissues at 1dpa were collected on ice using a BD Influx sorter. The viability of cells 94.5% was determined before loading cells into 10x Chromium platform.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP265421		loader:fastq load.py	L41598_S1_L001_I1_001.fastq.gz L41598_S1_L001_R1_001.fastq.gz L41598_S1_L001_R2_001.fastq.gz L41598_S1_L002_I1_001.fastq.gz L41598_S1_L002_R1_001.fastq.gz L41598_S1_L002_R2_001.fastq.gz L41598_S1_L003_I1_001.fastq.gz L41598_S1_L003_R1_001.fastq.gz L41598_S1_L003_R2_001.fastq.gz L41598_S1_L004_I1_001.fastq.gz L41598_S1_L004_R1_001.fastq.gz L41598_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	52222012142.0	411196946.0	L41598 S1 L001 I1 001.fastq.gz	0:8 1:28 2:91	A:10978857897;C:7760934381;G:8557391299;T:10029401940;N:92336569	8	28	91	10978857897	7760934381	8557391299	10029401940	92336569	SRX8434172	SRS6745285	SRA1081627	Stowers Institute for Medical Research\|Sanchez lab	Stowers Institute for Medical Research	1	0.92629	0.12539	0.78589	0.5225	91	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2020-08-11	Adult	Adult	Fin	Surface Structure

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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");;