metadata: run_metadata: 60 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue

60 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
11753	11753	ERR11758614	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S25_L001_R1_001.fastq.gz FliTp124hpf_S25_L001_R2_001.fastq.gz	fastq fastq	226833768.0	1800268.0	E MTAB 13196:FliTp124hpf S25 L001	0:28 1:98	A:65319978;C:50920193;G:49999849;T:60474280;N:119468	28	98	65319978	50920193	49999849	60474280	119468	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00122	0.88236	0.00056	0.09684	0.9978	0.89309	0.424	0.44186	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11754	11754	ERR11758619	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S27_L001_R1_001.fastq.gz FliTp124hpf_S27_L001_R2_001.fastq.gz	fastq fastq	261098334.0	2072209.0	E MTAB 13196:FliTp124hpf S27 L001	0:28 1:98	A:76098436;C:58031830;G:57099955;T:69729759;N:138354	28	98	76098436	58031830	57099955	69729759	138354	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00109	0.87641	0.00062	0.0976	0.99837	0.90065	0.45555	0.48712	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11755	11755	ERR11758589	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S16_L005_R1_001.fastq.gz FliTp124hpf_S16_L005_R2_001.fastq.gz	fastq fastq	1168367130.0	9272755.0	E MTAB 13196:FliTp124hpf S16 L005	0:28 1:98	A:323651598;C:269884286;G:268030176;T:306695030;N:106040	28	98	323651598	269884286	268030176	306695030	106040	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00491	0.90853	0.00131	0.07851	0.99019	0.84331	0.41536	0.48076	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11756	11756	ERR11758638	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S22_L001_R1_001.fastq.gz FliTp124hpf_S22_L001_R2_001.fastq.gz	fastq fastq	864786636.0	6863386.0	E MTAB 13196:FliTp124hpf S22 L001	0:28 1:98	A:241767760;C:198370882;G:198049093;T:226508751;N:90150	28	98	241767760	198370882	198049093	226508751	90150	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00375	0.89002	0.00114	0.0769	0.99237	0.84563	0.41796	0.48995	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11757	11757	ERR11758599	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S15_L005_R1_001.fastq.gz FliTp124hpf_S15_L005_R2_001.fastq.gz	fastq fastq	1795799502.0	14252377.0	E MTAB 13196:FliTp124hpf S15 L005	0:28 1:98	A:500590460;C:413239086;G:410401125;T:471402890;N:165941	28	98	500590460	413239086	410401125	471402890	165941	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00492	0.91242	0.0012	0.08044	0.99007	0.84668	0.42778	0.49291	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11758	11758	ERR11758601	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S26_L001_R1_001.fastq.gz FliTp124hpf_S26_L001_R2_001.fastq.gz	fastq fastq	266141358.0	2112233.0	E MTAB 13196:FliTp124hpf S26 L001	0:28 1:98	A:76996100;C:59592346;G:58963461;T:70457732;N:131719	28	98	76996100	59592346	58963461	70457732	131719	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00106	0.88422	0.00046	0.09358	0.99782	0.89449	0.47826	0.48948	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11759	11759	ERR11758630	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S14_L005_R1_001.fastq.gz FliTp124hpf_S14_L005_R2_001.fastq.gz	fastq fastq	1812847428.0	14387678.0	E MTAB 13196:FliTp124hpf S14 L005	0:28 1:98	A:502956890;C:417865079;G:416595454;T:475266679;N:163326	28	98	502956890	417865079	416595454	475266679	163326	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00483	0.91317	0.00123	0.07918	0.99036	0.84143	0.40704	0.4819	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11760	11760	ERR11758603	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S13_L005_R1_001.fastq.gz FliTp124hpf_S13_L005_R2_001.fastq.gz	fastq fastq	1544281830.0	12256205.0	E MTAB 13196:FliTp124hpf S13 L005	0:28 1:98	A:428008915;C:356252081;G:354333187;T:405545992;N:141655	28	98	428008915	356252081	354333187	405545992	141655	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00507	0.91025	0.00138	0.07858	0.98987	0.84295	0.41793	0.4891	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11761	11761	ERR11758613	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S21_L001_R1_001.fastq.gz FliTp124hpf_S21_L001_R2_001.fastq.gz	fastq fastq	761441436.0	6043186.0	E MTAB 13196:FliTp124hpf S21 L001	0:28 1:98	A:212876877;C:174700212;G:174244892;T:199537401;N:82054	28	98	212876877	174700212	174244892	199537401	82054	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00334	0.88899	0.00106	0.07762	0.99322	0.84476	0.42792	0.48783	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11762	11762	ERR11758645	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S23_L001_R1_001.fastq.gz FliTp124hpf_S23_L001_R2_001.fastq.gz	fastq fastq	873938772.0	6936022.0	E MTAB 13196:FliTp124hpf S23 L001	0:28 1:98	A:245075115;C:199879929;G:199312177;T:229576663;N:94888	28	98	245075115	199879929	199312177	229576663	94888	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00361	0.88671	0.00104	0.07855	0.99255	0.84723	0.41141	0.4885	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11763	11763	ERR11758598	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S28_L001_R1_001.fastq.gz FliTp124hpf_S28_L001_R2_001.fastq.gz	fastq fastq	164465532.0	1305282.0	E MTAB 13196:FliTp124hpf S28 L001	0:28 1:98	A:47319366;C:37063279;G:36394680;T:43602586;N:85621	28	98	47319366	37063279	36394680	43602586	85621	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00117	0.88222	0.00058	0.09358	0.99799	0.89217	0.54867	0.48545	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11764	11764	ERR11758593	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S24_L001_R1_001.fastq.gz FliTp124hpf_S24_L001_R2_001.fastq.gz	fastq fastq	558365976.0	4431476.0	E MTAB 13196:FliTp124hpf S24 L001	0:28 1:98	A:156054630;C:128109738;G:127885708;T:146256146;N:59754	28	98	156054630	128109738	127885708	146256146	59754	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00345	0.8879	0.00104	0.07718	0.99322	0.84364	0.38266	0.49193	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11765	11765	ERR11758635	ERX11157720	ERS16172938	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 wt 22hpf	SAMEA114192245	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192245\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 wt 22hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 wt 22hpf\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 wt 22hpf p	etv2 wt 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2Kaede_WT_S6_L001_R1_001.fastq.gz Etv2Kaede_WT_S6_L001_R2_001.fastq.gz	fastq fastq	1144014102.0	9079477.0	E MTAB 13196:Etv2Kaede WT S6 L001	0:28 1:98	A:316366230;C:260322813;G:259447166;T:307680623;N:197270	28	98	316366230	260322813	259447166	307680623	197270	ERX11157720	ERS16172938	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00336	0.89267	0.00137	0.13734	0.99545	0.81957	0.3734	0.53458	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11766	11766	ERR11758622	ERX11157720	ERS16172938	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 wt 22hpf	SAMEA114192245	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192245\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 wt 22hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 wt 22hpf\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 wt 22hpf p	etv2 wt 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2Kaede_WT_S8_L001_R2_001.fastq.gz Etv2Kaede_WT_S8_L001_R1_001.fastq.gz	fastq fastq	919270926.0	7295801.0	E MTAB 13196:Etv2Kaede WT S8 L001	0:28 1:98	A:259787542;C:207541571;G:206711907;T:245072713;N:157193	28	98	259787542	207541571	206711907	245072713	157193	ERX11157720	ERS16172938	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00358	0.88757	0.00137	0.15368	0.99551	0.83378	0.36405	0.53733	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11767	11767	ERR11758644	ERX11157720	ERS16172938	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 wt 22hpf	SAMEA114192245	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192245\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 wt 22hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 wt 22hpf\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 wt 22hpf p	etv2 wt 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2Kaede_WT_S5_L001_R2_001.fastq.gz Etv2Kaede_WT_S5_L001_R1_001.fastq.gz	fastq fastq	877658166.0	6965541.0	E MTAB 13196:Etv2Kaede WT S5 L001	0:28 1:98	A:243057461;C:199464116;G:198654377;T:236322700;N:159512	28	98	243057461	199464116	198654377	236322700	159512	ERX11157720	ERS16172938	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00328	0.88916	0.00127	0.13782	0.99559	0.81925	0.38227	0.53623	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11768	11768	ERR11758628	ERX11157720	ERS16172938	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 wt 22hpf	SAMEA114192245	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192245\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 wt 22hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 wt 22hpf\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 wt 22hpf p	etv2 wt 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2Kaede_WT_S7_L001_R1_001.fastq.gz Etv2Kaede_WT_S7_L001_R2_001.fastq.gz	fastq fastq	930443598.0	7384473.0	E MTAB 13196:Etv2Kaede WT S7 L001	0:28 1:98	A:258539610;C:211017108;G:209074684;T:251641766;N:170430	28	98	258539610	211017108	209074684	251641766	170430	ERX11157720	ERS16172938	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00355	0.88938	0.00148	0.14297	0.99569	0.83358	0.35626	0.53314	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11769	11769	ERR11758631	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S10_L001_R2_001.fastq.gz Etv2_Traver_S10_L001_R1_001.fastq.gz	fastq fastq	1947733326.0	15458201.0	E MTAB 13196:Etv2 Traver S10 L001	0:28 1:98	A:532150077;C:434208725;G:472140578;T:508906834;N:327112	28	98	532150077	434208725	472140578	508906834	327112	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00677	0.92596	0.00142	0.07895	0.98526	0.85123	0.42802	0.53518	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11770	11770	ERR11758646	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S28_L001_R2_001.fastq.gz Etv2_Traver_S28_L001_R1_001.fastq.gz	fastq fastq	1091426920.0	8801830.0	E MTAB 13196:Etv2 Traver S28 L001	0:26 1:98	A:302665480;C:247712584;G:269795015;T:271081940;N:171901	26	98	302665480	247712584	269795015	271081940	171901	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00585	0.90012	0.00149	0.07225	0.98746	0.84916	0.39007	0.54873	26	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11771	11771	ERR11758602	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S25_L001_R2_001.fastq.gz Etv2_Traver_S25_L001_R1_001.fastq.gz	fastq fastq	983616732.0	7932393.0	E MTAB 13196:Etv2 Traver S25 L001	0:26 1:98	A:272974243;C:222949925;G:242884450;T:244652916;N:155198	26	98	272974243	222949925	242884450	244652916	155198	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00571	0.90139	0.00143	0.07484	0.98756	0.85019	0.40119	0.54977	26	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11772	11772	ERR11758647	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S27_L001_R2_001.fastq.gz Etv2_Traver_S27_L001_R1_001.fastq.gz	fastq fastq	1162223232.0	9372768.0	E MTAB 13196:Etv2 Traver S27 L001	0:26 1:98	A:322910431;C:262934167;G:286614718;T:289578468;N:185448	26	98	322910431	262934167	286614718	289578468	185448	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00563	0.89924	0.00128	0.07464	0.98762	0.85064	0.38525	0.53889	26	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11773	11773	ERR11758634	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S12_L001_R2_001.fastq.gz Etv2_Traver_S12_L001_R1_001.fastq.gz	fastq fastq	1979462268.0	15710018.0	E MTAB 13196:Etv2 Traver S12 L001	0:28 1:98	A:539088187;C:442520328;G:480420115;T:517077908;N:355730	28	98	539088187	442520328	480420115	517077908	355730	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00707	0.9236	0.00137	0.07727	0.98451	0.85021	0.41845	0.56136	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11774	11774	ERR11758642	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S9_L001_R2_001.fastq.gz Etv2_Traver_S9_L001_R1_001.fastq.gz	fastq fastq	1809560214.0	14361589.0	E MTAB 13196:Etv2 Traver S9 L001	0:28 1:98	A:493206820;C:403886293;G:438502430;T:473641472;N:323199	28	98	493206820	403886293	438502430	473641472	323199	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00668	0.92354	0.00141	0.0785	0.98543	0.84938	0.43326	0.52002	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11775	11775	ERR11758623	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S26_L001_R2_001.fastq.gz Etv2_Traver_S26_L001_R1_001.fastq.gz	fastq fastq	1074533780.0	8665595.0	E MTAB 13196:Etv2 Traver S26 L001	0:26 1:98	A:298569273;C:243430874;G:265536499;T:266825982;N:171152	26	98	298569273	243430874	265536499	266825982	171152	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00579	0.90109	0.00136	0.07564	0.98788	0.85017	0.3554	0.54362	26	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11776	11776	ERR11758596	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S11_L001_R2_001.fastq.gz Etv2_Traver_S11_L001_R1_001.fastq.gz	fastq fastq	2167279758.0	17200633.0	E MTAB 13196:Etv2 Traver S11 L001	0:28 1:98	A:591928396;C:482735357;G:524267488;T:567952272;N:396245	28	98	591928396	482735357	524267488	567952272	396245	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00635	0.92351	0.00136	0.07835	0.9865	0.85204	0.41521	0.53672	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11777	11777	ERR11758595	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S36_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S36_L001_R1_001.fastq.gz	fastq fastq	211593816.0	1679316.0	E MTAB 13196:drl h2b dendra tb S36 L001	0:28 1:98	A:62689430;C:45809168;G:45709128;T:57272091;N:113999	28	98	62689430	45809168	45709128	57272091	113999	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00192	0.91331	0.00072	0.14588	0.99675	0.89292	0.51304	0.63144	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11778	11778	ERR11758629	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S37_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S37_L001_R1_001.fastq.gz	fastq fastq	980164836.0	7779086.0	E MTAB 13196:drl h2b dendra tb S37 L001	0:28 1:98	A:281375011;C:216067640;G:222839674;T:259781180;N:101331	28	98	281375011	216067640	222839674	259781180	101331	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00817	0.89718	0.00237	0.12153	0.98912	0.82643	0.46403	0.64954	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11779	11779	ERR11758618	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S39_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S39_L001_R1_001.fastq.gz	fastq fastq	12118302.0	96177.0	E MTAB 13196:drl h2b dendra tb S39 L001	0:28 1:98	A:3543790;C:2662872;G:2728134;T:3182383;N:1123	28	98	3543790	2662872	2728134	3182383	1123	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00786	0.88963	0.0025	0.12543	0.99403	0.88635	0.50098	0.64694	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11780	11780	ERR11758643	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S5_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S5_L005_R1_001.fastq.gz	fastq fastq	2061022698.0	16357323.0	E MTAB 13196:drl h2b dendra tb S5 L005	0:28 1:98	A:587730953;C:457631700;G:470283474;T:545196979;N:179592	28	98	587730953	457631700	470283474	545196979	179592	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.01192	0.91661	0.00336	0.12397	0.98518	0.82568	0.45692	0.65555	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11781	11781	ERR11758610	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S38_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S38_L001_R1_001.fastq.gz	fastq fastq	924603120.0	7338120.0	E MTAB 13196:drl h2b dendra tb S38 L001	0:28 1:98	A:265987815;C:203824483;G:210024160;T:244670646;N:96016	28	98	265987815	203824483	210024160	244670646	96016	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00773	0.89881	0.00242	0.12145	0.98944	0.82948	0.50529	0.66568	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11782	11782	ERR11758641	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S6_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S6_L005_R1_001.fastq.gz	fastq fastq	1954661562.0	15513187.0	E MTAB 13196:drl h2b dendra tb S6 L005	0:28 1:98	A:558769608;C:433724557;G:445550100;T:516443984;N:173313	28	98	558769608	433724557	445550100	516443984	173313	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0125	0.91697	0.00373	0.12359	0.98447	0.82558	0.4881	0.6456	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11783	11783	ERR11758591	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S35_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S35_L001_R1_001.fastq.gz	fastq fastq	4717188.0	37438.0	E MTAB 13196:drl h2b dendra tb S35 L001	0:28 1:98	A:1419430;C:1014265;G:1016661;T:1264642;N:2190	28	98	1419430	1014265	1016661	1264642	2190	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0012	0.65482	0.00054	0.10783	0.99953	0.97157	0.625	0.63689	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11784	11784	ERR11758606	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S34_L001_R1_001.fastq.gz drl_h2b-dendra_tb_S34_L001_R2_001.fastq.gz	fastq fastq	303645636.0	2409886.0	E MTAB 13196:drl h2b dendra tb S34 L001	0:28 1:98	A:90748559;C:65369482;G:65969002;T:81405258;N:153335	28	98	90748559	65369482	65969002	81405258	153335	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00228	0.91262	0.00099	0.14666	0.99638	0.89006	0.47177	0.63109	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11785	11785	ERR11758640	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S40_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S40_L001_R1_001.fastq.gz	fastq fastq	661361022.0	5248897.0	E MTAB 13196:drl h2b dendra tb S40 L001	0:28 1:98	A:190087869;C:145985661;G:150124621;T:175095762;N:67109	28	98	190087869	145985661	150124621	175095762	67109	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00785	0.89784	0.00251	0.12159	0.98948	0.83055	0.46095	0.64951	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11786	11786	ERR11758605	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S7_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S7_L005_R1_001.fastq.gz	fastq fastq	25157790.0	199665.0	E MTAB 13196:drl h2b dendra tb S7 L005	0:28 1:98	A:7330053;C:5600451;G:5635840;T:6589498;N:1948	28	98	7330053	5600451	5635840	6589498	1948	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.01201	0.91385	0.00341	0.12826	0.98595	0.85161	0.49226	0.64953	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11787	11787	ERR11758600	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S8_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S8_L005_R1_001.fastq.gz	fastq fastq	1422735804.0	11291554.0	E MTAB 13196:drl h2b dendra tb S8 L005	0:28 1:98	A:405788442;C:317299433;G:322206476;T:377317416;N:124037	28	98	405788442	317299433	322206476	377317416	124037	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.01226	0.91547	0.0037	0.12565	0.9849	0.83662	0.48279	0.64531	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11788	11788	ERR11758616	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S33_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S33_L001_R1_001.fastq.gz	fastq fastq	328918212.0	2610462.0	E MTAB 13196:drl h2b dendra tb S33 L001	0:28 1:98	A:98036464;C:71090137;G:71650807;T:87969481;N:171323	28	98	98036464	71090137	71650807	87969481	171323	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00197	0.89969	0.00087	0.14269	0.99681	0.89134	0.49763	0.63651	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11789	11789	ERR11758588	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S12_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S12_L005_R1_001.fastq.gz	fastq fastq	970032168.0	7698668.0	E MTAB 13196:drl h2b dendra 22hpf S12 L005	0:28 1:98	A:268176072;C:223973927;G:223251001;T:254545365;N:85803	28	98	268176072	223973927	223251001	254545365	85803	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00525	0.91336	0.00127	0.06812	0.98995	0.85395	0.40891	0.4918	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11790	11790	ERR11758597	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S42_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S42_L001_R1_001.fastq.gz	fastq fastq	716572206.0	5687081.0	E MTAB 13196:drl h2b dendra 22hpf S42 L001	0:28 1:98	A:198614388;C:164584363;G:164633280;T:188663484;N:76691	28	98	198614388	164584363	164633280	188663484	76691	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00366	0.8889	0.00092	0.06467	0.99261	0.84946	0.41353	0.49235	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11791	11791	ERR11758637	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S44_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S44_L001_R1_001.fastq.gz	fastq fastq	481216932.0	3819182.0	E MTAB 13196:drl h2b dendra 22hpf S44 L001	0:28 1:98	A:133704525;C:110630722;G:110586099;T:126246571;N:49015	28	98	133704525	110630722	110586099	126246571	49015	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00352	0.89199	0.00099	0.06481	0.99308	0.85251	0.50101	0.49137	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11792	11792	ERR11758617	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S41_L001_R1_001.fastq.gz drl_h2b-dendra_22hpf_S41_L001_R2_001.fastq.gz	fastq fastq	690504570.0	5480195.0	E MTAB 13196:drl h2b dendra 22hpf S41 L001	0:28 1:98	A:191676994;C:159013582;G:158945690;T:180795403;N:72901	28	98	191676994	159013582	158945690	180795403	72901	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00342	0.89103	0.00091	0.06637	0.99289	0.85196	0.42362	0.49417	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11793	11793	ERR11758627	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S10_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S10_L005_R1_001.fastq.gz	fastq fastq	1443584898.0	11457023.0	E MTAB 13196:drl h2b dendra 22hpf S10 L005	0:28 1:98	A:398056083;C:333283767;G:332935857;T:379178009;N:131182	28	98	398056083	333283767	332935857	379178009	131182	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00494	0.91295	0.00128	0.06617	0.99101	0.84855	0.40479	0.49207	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11794	11794	ERR11758609	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S40_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S40_L001_R1_001.fastq.gz	fastq fastq	139186908.0	1104658.0	E MTAB 13196:drl h2b dendra 22hpf S40 L001	0:28 1:98	A:39986504;C:31169749;G:30838192;T:37121531;N:70932	28	98	39986504	31169749	30838192	37121531	70932	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00113	0.88601	0.00057	0.08145	0.99801	0.89808	0.48148	0.48722	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11795	11795	ERR11758633	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S39_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S39_L001_R1_001.fastq.gz	fastq fastq	226310742.0	1796117.0	E MTAB 13196:drl h2b dendra 22hpf S39 L001	0:28 1:98	A:64619137;C:51094203;G:50285631;T:60191319;N:120452	28	98	64619137	51094203	50285631	60191319	120452	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00116	0.89046	0.00054	0.07999	0.99797	0.89739	0.58119	0.48393	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11796	11796	ERR11758604	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S9_L005_R1_001.fastq.gz drl_h2b-dendra_22hpf_S9_L005_R2_001.fastq.gz	fastq fastq	1419705504.0	11267504.0	E MTAB 13196:drl h2b dendra 22hpf S9 L005	0:28 1:98	A:390831393;C:328833478;G:328344998;T:371567158;N:128477	28	98	390831393	328833478	328344998	371567158	128477	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00519	0.91357	0.00132	0.0668	0.99042	0.84883	0.46254	0.47002	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11797	11797	ERR11758608	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S43_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S43_L001_R1_001.fastq.gz	fastq fastq	744179814.0	5906189.0	E MTAB 13196:drl h2b dendra 22hpf S43 L001	0:28 1:98	A:206745595;C:171274047;G:171089532;T:194990120;N:80520	28	98	206745595	171274047	171089532	194990120	80520	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0033	0.89238	0.00092	0.06573	0.99348	0.85307	0.42184	0.45487	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11798	11798	ERR11758625	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S11_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S11_L005_R1_001.fastq.gz	fastq fastq	1552027554.0	12317679.0	E MTAB 13196:drl h2b dendra 22hpf S11 L005	0:28 1:98	A:428241149;C:359820303;G:356746163;T:407080418;N:139521	28	98	428241149	359820303	356746163	407080418	139521	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00528	0.91344	0.00122	0.06856	0.98946	0.85667	0.46289	0.49059	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11799	11799	ERR11758594	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S37_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S37_L001_R1_001.fastq.gz	fastq fastq	193604292.0	1536542.0	E MTAB 13196:drl h2b dendra 22hpf S37 L001	0:28 1:98	A:55140258;C:43966158;G:43414595;T:50989845;N:93436	28	98	55140258	43966158	43414595	50989845	93436	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00128	0.89527	0.00063	0.07949	0.99774	0.89538	0.424	0.48666	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11800	11800	ERR11758639	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S38_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S38_L001_R1_001.fastq.gz	fastq fastq	226896894.0	1800769.0	E MTAB 13196:drl h2b dendra 22hpf S38 L001	0:28 1:98	A:65107594;C:50761930;G:50291626;T:60619991;N:115753	28	98	65107594	50761930	50291626	60619991	115753	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00111	0.88883	0.00057	0.07885	0.99807	0.89412	0.53921	0.47439	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11801	11801	ERR11758636	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S31_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S31_L001_R2_001.fastq.gz	fastq fastq	188521452.0	1496202.0	E MTAB 13196:drl h2b dendra 12somites S31 L001	0:28 1:98	A:54946745;C:39757518;G:41515822;T:52209939;N:91428	28	98	54946745	39757518	41515822	52209939	91428	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00175	0.90844	0.00064	0.15428	0.99636	0.86393	0.39351	0.52017	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11802	11802	ERR11758612	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S35_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S35_L001_R1_001.fastq.gz	fastq fastq	671596632.0	5330132.0	E MTAB 13196:drl h2b dendra 12somites S35 L001	0:28 1:98	A:189747551;C:145545792;G:153208485;T:183026617;N:68187	28	98	189747551	145545792	153208485	183026617	68187	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00594	0.90285	0.00156	0.12933	0.98823	0.80955	0.40956	0.53154	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11803	11803	ERR11758620	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S36_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S36_L001_R1_001.fastq.gz	fastq fastq	456194592.0	3620592.0	E MTAB 13196:drl h2b dendra 12somites S36 L001	0:28 1:98	A:129689128;C:98798602;G:103687645;T:123970211;N:49006	28	98	129689128	98798602	103687645	123970211	49006	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00578	0.90274	0.00162	0.13523	0.98859	0.81917	0.43296	0.52776	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11804	11804	ERR11758607	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S1_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S1_L005_R1_001.fastq.gz	fastq fastq	1313559828.0	10425078.0	E MTAB 13196:drl h2b dendra 12somites S1 L005	0:28 1:98	A:369071579;C:285484861;G:298845646;T:360037984;N:119758	28	98	369071579	285484861	298845646	360037984	119758	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00866	0.92327	0.00213	0.13248	0.98374	0.80846	0.41836	0.52646	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11805	11805	ERR11758621	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S3_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S3_L005_R1_001.fastq.gz	fastq fastq	1400830452.0	11117702.0	E MTAB 13196:drl h2b dendra 12somites S3 L005	0:28 1:98	A:392932148;C:304653102;G:320171450;T:382949722;N:124030	28	98	392932148	304653102	320171450	382949722	124030	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0091	0.92525	0.00221	0.13204	0.98328	0.80683	0.39896	0.52474	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11806	11806	ERR11758615	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S32_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S32_L001_R1_001.fastq.gz	fastq fastq	130164930.0	1033055.0	E MTAB 13196:drl h2b dendra 12somites S32 L001	0:28 1:98	A:38325421;C:27354135;G:28209607;T:36209402;N:66365	28	98	38325421	27354135	28209607	36209402	66365	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00164	0.90364	0.00061	0.16156	0.99651	0.87846	0.37878	0.51845	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11807	11807	ERR11758590	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S34_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S34_L001_R1_001.fastq.gz	fastq fastq	806214402.0	6398527.0	E MTAB 13196:drl h2b dendra 12somites S34 L001	0:28 1:98	A:227716399;C:174839165;G:184278464;T:219297626;N:82748	28	98	227716399	174839165	184278464	219297626	82748	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00622	0.9021	0.00153	0.13047	0.98772	0.80866	0.40065	0.53454	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11808	11808	ERR11758624	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S33_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S33_L001_R1_001.fastq.gz	fastq fastq	633634974.0	5028849.0	E MTAB 13196:drl h2b dendra 12somites S33 L001	0:28 1:98	A:179249875;C:137201579;G:144307176;T:172806546;N:69798	28	98	179249875	137201579	144307176	172806546	69798	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00585	0.90174	0.00155	0.12966	0.98831	0.80888	0.45862	0.52706	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11809	11809	ERR11758626	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S4_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S4_L005_R1_001.fastq.gz	fastq fastq	927876096.0	7364096.0	E MTAB 13196:drl h2b dendra 12somites S4 L005	0:28 1:98	A:261732233;C:201837729;G:210685660;T:253535088;N:85386	28	98	261732233	201837729	210685660	253535088	85386	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00851	0.92329	0.00197	0.13519	0.98378	0.81665	0.41822	0.52852	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11810	11810	ERR11758632	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S29_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S29_L001_R2_001.fastq.gz	fastq fastq	213074064.0	1691064.0	E MTAB 13196:drl h2b dendra 12somites S29 L001	0:28 1:98	A:62826305;C:44807633;G:46218609;T:59105445;N:116072	28	98	62826305	44807633	46218609	59105445	116072	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00163	0.90265	0.00072	0.1535	0.99701	0.87241	0.47674	0.51858	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11811	11811	ERR11758592	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S2_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S2_L005_R1_001.fastq.gz	fastq fastq	1647474570.0	13075195.0	E MTAB 13196:drl h2b dendra 12somites S2 L005	0:28 1:98	A:462072903;C:358669639;G:376971859;T:449610611;N:149558	28	98	462072903	358669639	376971859	449610611	149558	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0086	0.92221	0.00193	0.12995	0.98285	0.80275	0.43249	0.52848	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11812	11812	ERR11758611	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S30_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S30_L001_R2_001.fastq.gz	fastq fastq	223279938.0	1772063.0	E MTAB 13196:drl h2b dendra 12somites S30 L001	0:28 1:98	A:64875575;C:47356253;G:49541812;T:61396530;N:109768	28	98	64875575	47356253	49541812	61396530	109768	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00168	0.90617	0.00068	0.15194	0.99669	0.86052	0.46907	0.52824	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	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");;