metadata: run_metadata: 42 rows where experiment.library_selection = "RANDOM", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and experiment.platform = "ILLUMINA"

42 rows where experiment.library_selection = "RANDOM", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and experiment.platform = "ILLUMINA"

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.attributes	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.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
10060	10060	ERR4795364	ERX4665135	ERS5281176	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 4	E MTAB 9727:Sample 4		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 4 s	Sample 4 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz	fastq	5410723202.0	71707309.0	E MTAB 9727:Sample 4	0:75.46 1:0	A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666	75	0		1330416803	531269504	734031980	2814959249	45666	ERX4665135	ERS5281176	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.33614		0.21532		0.99019		0.41002		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10061	10061	ERR4795365	ERX4665135	ERS5281176	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 4	E MTAB 9727:Sample 4		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 4 s	Sample 4 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz	fastq	5414184547.0	71707309.0	E MTAB 9727:Sample 4 1	0:0 1:75.50	A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967	0	75		1582938104	1052565419	1177180395	1600161662	1338967	ERX4665135	ERS5281176	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.84976		0.28521		0.85038		0.5124		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10062	10062	ERR4795362	ERX4665134	ERS5281175	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 3	E MTAB 9727:Sample 3		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 3 s	Sample 3 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz	fastq	4823193891.0	63965519.0	E MTAB 9727:Sample 3	0:75.40 1:0	A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086	75	0		1323978162	446831209	581746343	2470114091	524086	ERX4665134	ERS5281175	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.36549		0.19722		0.95552		0.4702		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10063	10063	ERR4795363	ERX4665134	ERS5281175	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 3	E MTAB 9727:Sample 3		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 3 s	Sample 3 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz	fastq	4828889391.0	63965519.0	E MTAB 9727:Sample 3 1	0:0 1:75.49	A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756	0	75		1434099697	964508763	893584575	1534727600	1968756	ERX4665134	ERS5281175	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.85811		0.26231		0.82731		0.48618		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10064	10064	ERR4795360	ERX4665133	ERS5281174	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 2	E MTAB 9727:Sample 2		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 2 s	Sample 2 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz	fastq	5598371393.0	74235388.0	E MTAB 9727:Sample 2	0:75.41 1:0	A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655	75	0		1526486973	558020193	717587491	2795646081	630655	ERX4665133	ERS5281174	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.28059		0.19252		0.96404		0.4874		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10065	10065	ERR4795361	ERX4665133	ERS5281174	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 2	E MTAB 9727:Sample 2		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 2 s	Sample 2 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz	fastq	5600151371.0	74235388.0	E MTAB 9727:Sample 2 1	0:0 1:75.44	A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060	0	75		1850568176	1035622971	1071138281	1640475883	2346060	ERX4665133	ERS5281174	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.7679		0.30371		0.82651		0.43401		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10066	10066	ERR4795358	ERX4665132	ERS5281173	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 1	E MTAB 9727:Sample 1		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 1 s	Sample 1 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz	fastq	4996502316.0	66258508.0	E MTAB 9727:Sample 1	0:75.41 1:0	A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936	75	0		1330744174	451622042	591151500	2622422664	561936	ERX4665132	ERS5281173	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.29754		0.17671		0.9669		0.45463		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10067	10067	ERR4795359	ERX4665132	ERS5281173	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 1	E MTAB 9727:Sample 1		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 1 s	Sample 1 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz	fastq	4999908389.0	66258508.0	E MTAB 9727:Sample 1 1	0:0 1:75.46	A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512	0	75		1591945117	933968124	986108614	1485824022	2062512	ERX4665132	ERS5281173	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.81333		0.2466		0.83027		0.51572		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
11238	11238	ERR10782555	ERX10233132	ERS14439197	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 6	E MTAB 12503:Sample 6		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 6\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 6 p	Sample 6 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz	fastq fastq	14809693138.0	49038719.0	E MTAB 12503:20170530.A 6 R	0:151 1:151	A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269	151	151		4069749497	3367864217	3430269434	3928390721	13419269	ERX10233132	ERS14439197	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.83945	0.69977	0.27269	0.22488	0.74523	0.77654	0.4899	0.4358	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11239	11239	ERR10782554	ERX10233131	ERS14439196	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 5	E MTAB 12503:Sample 5		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 5\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 5 p	Sample 5 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz	fastq fastq	14954968728.0	49519764.0	E MTAB 12503:20170530.A 5 R	0:151 1:151	A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280	151	151		4063340262	3440933120	3455723079	3981396987	13575280	ERX10233131	ERS14439196	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.85891	0.86859	0.28842	0.28866	0.7349	0.75051	0.45532	0.49145	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11240	11240	ERR10782553	ERX10233130	ERS14439195	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 2	E MTAB 12503:Sample 2		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 2\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 2 p	Sample 2 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz	fastq fastq	16267571562.0	53866131.0	E MTAB 12503:20170530.A 2 R	0:151 1:151	A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668	151	151		4395815325	3765428574	3780844712	4310729283	14753668	ERX10233130	ERS14439195	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.86977	0.8727	0.28497	0.28427	0.70763	0.72301	0.47478	0.47986	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11241	11241	ERR10782552	ERX10233129	ERS14439194	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 1	E MTAB 12503:Sample 1		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 1\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 1 p	Sample 1 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz	fastq fastq	15446599662.0	51147681.0	E MTAB 12503:20170530.A 1 R	0:151 1:151	A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332	151	151		4289931639	3451135010	3474244788	4217248893	14039332	ERX10233129	ERS14439194	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.90114	0.90507	0.32128	0.32127	0.70232	0.71956	0.47336	0.47528	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11242	11242	ERR10782551	ERX10233128	ERS14439193	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 7	E MTAB 12503:Sample 7		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 7\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 7 p	Sample 7 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz	fastq fastq	12726557236.0	42140918.0	E MTAB 12503:20170530.A 7 R	0:151 1:151	A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382	151	151		3510176970	2879679978	2932244172	3392911734	11544382	ERX10233128	ERS14439193	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.88531	0.88678	0.33279	0.3329	0.73545	0.74992	0.52548	0.52864	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11243	11243	ERR10782550	ERX10233127	ERS14439192	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 4	E MTAB 12503:Sample 4		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 4\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 4 p	Sample 4 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz	fastq fastq	15697575554.0	51978727.0	E MTAB 12503:20170530.A 4 R	0:151 1:151	A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133	151	151		4256444510	3622485921	3650190489	4154211501	14243133	ERX10233127	ERS14439192	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.87714	0.88071	0.29319	0.29235	0.69844	0.7164	0.47594	0.47385	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11244	11244	ERR10782549	ERX10233126	ERS14439191	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 3	E MTAB 12503:Sample 3		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 3\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 3 p	Sample 3 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz	fastq fastq	13839085674.0	45824787.0	E MTAB 12503:20170530.A 3 R	0:151 1:151	A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362	151	151		3812423011	3120168590	3163957945	3729983766	12552362	ERX10233126	ERS14439191	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.88987	0.74432	0.33651	0.27875	0.69229	0.72934	0.46981	0.46116	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
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
34262	34262	SRR31595085	SRX26959911	SRS23429841	SRP549196	PRJNA1193812	Single cell transcriptome sequencing of zebrafish olfactory epithelium	PRJNA1193812	Other	We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.		Alarm substances treatment Group		CAS		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:1 year old\|dev stage:adult CAS group\|collection date:2020 10 10\|geo loc name:China: Wuhan\|sex:male\|tissue:Olfactory epithelium CAS group\|BioSampleModel:Model organism or animal	Single cell transcriptome of the AB zebrafish olfactory epithelium post treatment with alarm substances	CAS OE	CAS OE	sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	NextSeq 550	SRP549196			CAS_S1_L001_R1_001.fastq.gz CAS_S1_L001_R2_001.fastq.gz	fastq fastq	54518124857.0	458135503.0	CAS S1 L001 R1 001.fastq.gz	0:28 1:91	A:15384916510;C:12274547586;G:14008767028;T:12837270924;N:12622809	28	91		15384916510	12274547586	14008767028	12837270924	12622809	SRX26959911	SRS23429841	SRA2027027	Institute of Hydrobiology, Chinese Academy of Sciences\|Chinese Academy of Sciences	Institute of Hydrobiology, Chinese Academy of Sciences												T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2024-12-04	Adult	Adult	Brain	Nervous System
34263	34263	SRR31595086	SRX26959910	SRS23429840	SRP549196	PRJNA1193812	Single cell transcriptome sequencing of zebrafish olfactory epithelium	PRJNA1193812	Other	We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.		Blank control group		CTR		strain:AB strain\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:1 year old\|dev stage:adult CTR group\|collection date:2020 10 10\|geo loc name:China: Wuhan\|sex:male\|tissue:Olfactory epithelium CTR group\|BioSampleModel:Model organism or animal	Single cell transcriptome of the AB strain zebrafish olfactory epithelium	CTR OE	CTR OE	sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	NextSeq 550	SRP549196			CTR_S1_L001_R1_001.fastq.gz CTR_S1_L001_R2_001.fastq.gz	fastq fastq	50773421790.0	426667410.0	CTR S1 L001 R1 001.fastq.gz	0:28 1:91	A:14105926130;C:11510784907;G:13135577448;T:12011516484;N:9616821	28	91		14105926130	11510784907	13135577448	12011516484	9616821	SRX26959910	SRS23429840	SRA2027027	Institute of Hydrobiology, Chinese Academy of Sciences\|Chinese Academy of Sciences	Institute of Hydrobiology, Chinese Academy of Sciences												T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2024-12-04	Adult	Adult	Brain	Nervous 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
68777	68777	SRR18188990	SRX14335888	SRS12150682	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.				GC9		strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate3\|BioSampleModel:Model organism or animal	3pgc	3 3pgc	3 3pgc	primordial germ cell from 5 hpf zebrafish embryos			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100			GC9_R1.fq.gz GC9_R2.fq.gz	fastq fastq	16392678600.0	54642262.0	GC9 R1.fq.gz	0:150 1:150	A:4548403510;C:3786937912;G:3801036342;T:4255236177;N:1064659	150	150		4548403510	3786937912	3801036342	4255236177	1064659	SRX14335888	SRS12150682	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.92711	0.93044	0.08622	0.08652	0.79693	0.80306	0.58096	0.58168	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System
68778	68778	SRR18188991	SRX14335887	SRS12150683	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.				GC4		strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate2\|BioSampleModel:Model organism or animal	2pgc	2 2pgc	2 2pgc	primordial germ cell from 5 hpf zebrafish embryos			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100			GC4_R1.fq.gz GC4_R2.fq.gz	fastq fastq	14471348700.0	48237829.0	GC4 R1.fq.gz	0:150 1:150	A:4127039158;C:3211803959;G:3224340004;T:3907215356;N:950223	150	150		4127039158	3211803959	3224340004	3907215356	950223	SRX14335887	SRS12150683	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.91951	0.91886	0.14001	0.14043	0.75777	0.76605	0.55643	0.55313	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System
68779	68779	SRR18188992	SRX14335886	SRS12150681	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.				GC1		strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate1\|BioSampleModel:Model organism or animal	1pgc	1 1pgc	1 1pgc	primordial germ cell from 5 hpf zebrafish embryos			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100			GC1_R1.fq.gz GC1_R2.fq.gz	fastq fastq	18801698100.0	62672327.0	GC1 R1.fq.gz	0:150 1:150	A:5242992703;C:4310290517;G:4334163362;T:4913025193;N:1226325	150	150		5242992703	4310290517	4334163362	4913025193	1226325	SRX14335886	SRS12150681	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.93192	0.93277	0.09532	0.09559	0.78358	0.7906	0.5661	0.56344	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System
71597	71597	SRR21780858	SRX17775679	SRS15301946	SRP400655	PRJNA885906	Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish	PRJNA885906	Other	The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.			BefA diss	BefA 1532		strain:Tgins; eGFP\|dev stage:6dpf\|sex:not applicable\|tissue:dissected digestive systems\|BioSampleModel:Model organism or animal	germ free 6dpf dissected digestive systems treated with protein	1532	1532	the cells are from dissected guts from germ free larvae but were treated with exogenous protein			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP400655			BefAdiss_S2_L008_R1_001.fastq.gz BefAdiss_S2_L008_R2_001.fastq.gz	fastq fastq	62618506720.0	355786970.0	BefAdiss S2 L008 R1 001.fastq.gz	0:26 1:150	A:18434729847;C:13374700052;G:13922149278;T:16789619859;N:97307684	26	150		18434729847	13374700052	13922149278	16789619859	97307684	SRX17775679	SRS15301946	SRA1511285	University of Oregon\|Institute of Molecular Biology	University of Oregon	2	0.00182	0.89692	0.00064	0.07716	0.9962	0.82798	0.42608	0.6075	26	150	T	B	sc-like readlen	illumina	hiseq_era	unknown	random_priming	unknown	sc	unknown	unknown	United States	2022-10-02	Larval	Larval	Gut	Digestive System
71598	71598	SRR21780859	SRX17775678	SRS15301945	SRP400655	PRJNA885906	Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish	PRJNA885906	Other	The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.			GF diss2	GF 1531		strain:Tgins; eGFP\|dev stage:6dpf\|sex:not applicable\|tissue:dissected digestive systems\|BioSampleModel:Model organism or animal	germ free 6dpf dissected digestive systems lane 2	1531	1531	the cells dissected guts from germ free larvae were split across two lanes library 1530/1531 come from same sample			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP400655			GFdiss2_S1_L004_R1_001.fastq.gz GFdiss2_S1_L004_R2_001.fastq.gz	fastq fastq	66862372720.0	379899845.0	GFdiss2 S1 L004 R1 001.fastq.gz	0:26 1:150	A:10814720171;C:8609009803;G:8785194946;T:9942289999;N:28711157801	26	150		10814720171	8609009803	8785194946	9942289999	28711157801	SRX17775678	SRS15301945	SRA1511285	University of Oregon\|Institute of Molecular Biology	University of Oregon	2	0.00191	0.92014	0.00074	0.08575	0.99616	0.87793	0.35964	0.58459	26	150	T	B	sc-like readlen	illumina	hiseq_era	unknown	random_priming	unknown	sc	unknown	unknown	United States	2022-10-02	Larval	Larval	Gut	Digestive System
71599	71599	SRR21780860	SRX17775677	SRS15301944	SRP400655	PRJNA885906	Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish	PRJNA885906	Other	The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.			GF diss1	GF 1530		strain:Tgins; eGFP\|dev stage:6dpf\|sex:not applicable\|tissue:dissected digestive systems\|BioSampleModel:Model organism or animal	germ free 6dpf dissected digestive systems lane 1	1530	1530	the cells dissected guts from germ free larvae were split across two lanes library 1530/1531 come from same sample			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP400655			GFdiss1_S1_L007_R1_001.fastq.gz GFdiss1_S1_L007_R2_001.fastq.gz	fastq fastq	63769716736.0	362327936.0	GFdiss1 S1 L007 R1 001.fastq.gz	0:26 1:150	A:18291156920;C:14095548431;G:14421791117;T:16786925671;N:174294597	26	150		18291156920	14095548431	14421791117	16786925671	174294597	SRX17775677	SRS15301944	SRA1511285	University of Oregon\|Institute of Molecular Biology	University of Oregon	2	0.00172	0.91725	0.00064	0.08763	0.99648	0.82804	0.39234	0.5982	26	150	T	B	sc-like readlen	illumina	hiseq_era	unknown	random_priming	unknown	sc	unknown	unknown	United States	2022-10-02	Larval	Larval	Gut	Digestive System
71600	71600	SRR21780861	SRX17775676	SRS15301943	SRP400655	PRJNA885906	Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish	PRJNA885906	Other	The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.			GF1	GF1 HWLY5BBXX		strain:Tgnkx2.2a; eGFP\|dev stage:6dpf\|sex:not applicable\|tissue:whole larvae\|BioSampleModel:Model organism or animal	germ free no microbiota 6dpf whole larvae	HWLY5BBXX GF1	HWLY5BBXX GF1	data is culmination of two HiSeq4000 runs. One run CV/GF samples were both run on the same line and in the second run CV/GF samples were run on individual lanes. Data was demultiplexed and treatment groups combined for total number of reads per group to be above spec.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP400655			GF1_S2_L006_R2_001.fastq.gz GF1_S2_L006_R1_001.fastq.gz	fastq fastq	43844549700.0	146148499.0	GF1 S2 L006 R1 001.fastq.gz	0:150 1:150	A:10577324109;C:7388773641;G:8146030296;T:17727050506;N:5371148	150	150		10577324109	7388773641	8146030296	17727050506	5371148	SRX17775676	SRS15301943	SRA1511285	University of Oregon\|Institute of Molecular Biology	University of Oregon	2	0.02507	0.90549	0.00575	0.09697	0.99348	0.79091	0.53513	0.47471	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	unknown	unknown	United States	2022-10-02	Larval	Larval	Whole Organism	All anatomical structures
71601	71601	SRR21780862	SRX17775675	SRS15301942	SRP400655	PRJNA885906	Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish	PRJNA885906	Other	The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.			CV2	CV2 HWLY5BBXX		strain:Tgnkx2.2a; eGFP\|dev stage:6dpf\|sex:not applicable\|tissue:whole larvae\|BioSampleModel:Model organism or animal	conventional 6dpf whole larvae	HWLY5BBXX CV2	HWLY5BBXX CV2	data is culmination of two HiSeq4000 runs. One run CV/GF samples were both run on the same line and in the second run CV/GF samples were run on individual lanes. Data was demultiplexed and treatment groups combined for total number of reads per group to be above spec.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP400655			CV2_S1_L006_R1_001.fastq.gz CV2_S1_L006_R2_001.fastq.gz	fastq fastq	42260060400.0	140866868.0	CV2 S1 L006 R1 001.fastq.gz	0:150 1:150	A:10306378433;C:7083604228;G:7794391616;T:17070639212;N:5046911	150	150		10306378433	7083604228	7794391616	17070639212	5046911	SRX17775675	SRS15301942	SRA1511285	University of Oregon\|Institute of Molecular Biology	University of Oregon	2	0.0311	0.89818	0.0069	0.11191	0.99257	0.78642	0.52164	0.50459	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	unknown	unknown	United States	2022-10-02	Larval	Larval	Whole Organism	All anatomical structures

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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");;