metadata: run_metadata: 377 rows where experiment.library_layout = "PAIRED", technology = "10x" and tissue

377 rows where experiment.library_layout = "PAIRED", technology = "10x" 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	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
25127	25127	SRR25610724	SRX21337840	SRS18583009	SRP454647	PRJNA1004574	Gene expression profile at single cell level of mitfa:GFP labelled zebrafish cells at 24hpf	GSE240655	Transcriptome Analysis	Melanocytes of the skin have traditionally been viewed as a homogeneous population however recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study we utilized a transgenic zebrafish line Tgmifa:GFP that expresses green fluorescent protein GFP under the control of a melanocyte specific promoter mitfa labelling only those cells in which mitfa promoter is active. We then performed single cell RNA sequencing scRNA seq analysis to explore the diversity of mitfa:GFP positive cells. Overall design: Tgmitfa:GFP zebrafish embryos were raised till 24 hpf and then the cells were isolated. The cells expressing mitfa:GFP were then sorted into low and high GFP population using a flow cytometer	parent bioproject:PRJNA975369	pubmed:39163475		mitfa high zf scRNAseq	GSM7706847		tissue:mitfa:GFP+ cells\|genotype:Tgmitfa:GFP\|cell type:mitfa:GFP+ cells\|population:mitfa:GFP high\|age:24 hpf loc name:missing\|collection date:missing	mitfa high zf scRNAseq	The demultiplexing barcode processing gene counting and aggregation were done using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	mitfa:GFP+ cells		Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter’s instructions single cell 3’ v3.1 single index protocol 10x Genomics. Briefly 24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and sample index were added.		genotype:Tgmitfa:GFP\|cell type:mitfa:GFP+ cells\|population:mitfa:GFP high\|age:24 hpf	GSM7706847	GSM7706847: mitfa high zf scRNAseq; Danio rerio; RNA Seq	GSM7706847 r1	GSM7706847	1	Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter's instructions single cell three prime v3.1 single index protocol 10x Genomics. Briefly 24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and sample index were added.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP454647		loader:fastq load.py	HM_S4_L001_I1_001.fastq.gz HM_S4_L001_R1_001.fastq.gz HM_S4_L001_R2_001.fastq.gz	fastq fastq fastq	24842565758.0	195610754.0	GSM7706847 r1	0:8 1:28 2:91	A:5175410152;C:3650416721;G:4658958024;T:4315769305;N:24412	8	28	91	5175410152	3650416721	4658958024	4315769305	24412	SRX21337840	SRS18583009	SRA1691286	Pigment Cell Biology Lab, CSIR-IGIB	Pigment Cell Biology Lab, CSIR-IGIB	1	0.84133		0.13672		0.84756		0.52135		91		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	unknown	sc	single_cell_droplet	10x	India	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25128	25128	SRR25610725	SRX21337839	SRS18583008	SRP454647	PRJNA1004574	Gene expression profile at single cell level of mitfa:GFP labelled zebrafish cells at 24hpf	GSE240655	Transcriptome Analysis	Melanocytes of the skin have traditionally been viewed as a homogeneous population however recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study we utilized a transgenic zebrafish line Tgmifa:GFP that expresses green fluorescent protein GFP under the control of a melanocyte specific promoter mitfa labelling only those cells in which mitfa promoter is active. We then performed single cell RNA sequencing scRNA seq analysis to explore the diversity of mitfa:GFP positive cells. Overall design: Tgmitfa:GFP zebrafish embryos were raised till 24 hpf and then the cells were isolated. The cells expressing mitfa:GFP were then sorted into low and high GFP population using a flow cytometer	parent bioproject:PRJNA975369	pubmed:39163475		mitfa low zf scRNAseq	GSM7706846		tissue:mitfa:GFP+ cells\|genotype:Tgmitfa:GFP\|cell type:mitfa:GFP+ cells\|population:mitfa:GFP low\|age:24 hpf loc name:missing\|collection date:missing	mitfa low zf scRNAseq	The demultiplexing barcode processing gene counting and aggregation were done using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	mitfa:GFP+ cells		Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter’s instructions single cell 3’ v3.1 single index protocol 10x Genomics. Briefly 24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and sample index were added.		genotype:Tgmitfa:GFP\|cell type:mitfa:GFP+ cells\|population:mitfa:GFP low\|age:24 hpf	GSM7706846	GSM7706846: mitfa low zf scRNAseq; Danio rerio; RNA Seq	GSM7706846 r1	GSM7706846	1	Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter's instructions single cell three prime v3.1 single index protocol 10x Genomics. Briefly 24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and sample index were added.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP454647		loader:fastq load.py	LM_S3_L001_R2_001.fastq.gz LM_S3_L001_R1_001.fastq.gz LM_S3_L001_I1_001.fastq.gz	fastq fastq fastq	17519211850.0	137946550.0	GSM7706846 r1	0:8 1:28 2:91	A:3674575574;C:2564940740;G:3313017210;T:3000585838;N:16688	8	28	91	3674575574	2564940740	3313017210	3000585838	16688	SRX21337839	SRS18583008	SRA1691286	Pigment Cell Biology Lab, CSIR-IGIB	Pigment Cell Biology Lab, CSIR-IGIB	1	0.81163		0.13698		0.859		0.52032		91		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	unknown	sc	single_cell_droplet	10x	India	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25129	25129	SRR25619749	SRX21346683	SRS18591743	SRP454714	PRJNA1004663	Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival	GSE240721	Other	Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach we demonstrate that larval RBs in zebrafish fall into three largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib which is used in clinic and causes peripheral neuropathy. Importantly dovitinib mediated axon loss can be suppressed by loss of Sarm1 a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solu…				30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	GSM7708237		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM7708237	GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq; Danio rerio; RNA Seq	GSM7708237 r1	GSM7708237	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454714		loader:fastq load.py	CEL201106AN_WT-2_S20_L004_R2_001.fastq.gz CEL201106AN_WT-2_S20_L004_R1_001.fastq.gz CEL201106AN_WT-2_S20_L004_I1_001.fastq.gz	fastq fastq fastq	17931740743.0	141194809.0	GSM7708237 r1	0:8 1:28 2:91	A:3982504087;C:2545259636;G:2793618614;T:3526744725;N:600557	8	28	91	3982504087	2545259636	2793618614	3526744725	600557	SRX21346683	SRS18591743	SRA1691311	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.87401		0.26924		0.7517		0.5102		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25130	25130	SRR25619750	SRX21346683	SRS18591743	SRP454714	PRJNA1004663	Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival	GSE240721	Other	Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach we demonstrate that larval RBs in zebrafish fall into three largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib which is used in clinic and causes peripheral neuropathy. Importantly dovitinib mediated axon loss can be suppressed by loss of Sarm1 a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solu…				30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	GSM7708237		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM7708237	GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq; Danio rerio; RNA Seq	GSM7708237 r1	GSM7708237	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454714		loader:fastq load.py	CEL201106AN_WT-2_S19_L004_I1_001.fastq.gz CEL201106AN_WT-2_S19_L004_R1_001.fastq.gz CEL201106AN_WT-2_S19_L004_R2_001.fastq.gz	fastq fastq fastq	15740158766.0	123938258.0	GSM7708237 r2	0:8 1:28 2:91	A:3499017196;C:2231848518;G:2450171440;T:3096822046;N:522278	8	28	91	3499017196	2231848518	2450171440	3096822046	522278	SRX21346683	SRS18591743	SRA1691311	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.87457		0.27073		0.75278		0.50801		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25131	25131	SRR25619751	SRX21346683	SRS18591743	SRP454714	PRJNA1004663	Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival	GSE240721	Other	Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach we demonstrate that larval RBs in zebrafish fall into three largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib which is used in clinic and causes peripheral neuropathy. Importantly dovitinib mediated axon loss can be suppressed by loss of Sarm1 a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solu…				30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	GSM7708237		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM7708237	GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq; Danio rerio; RNA Seq	GSM7708237 r1	GSM7708237	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454714		loader:fastq load.py	CEL201106AN_WT-2_S18_L004_R2_001.fastq.gz CEL201106AN_WT-2_S18_L004_R1_001.fastq.gz CEL201106AN_WT-2_S18_L004_I1_001.fastq.gz	fastq fastq fastq	14146022254.0	111386002.0	GSM7708237 r3	0:8 1:28 2:91	A:3147384451;C:2003642594;G:2200506573;T:2784120122;N:472442	8	28	91	3147384451	2003642594	2200506573	2784120122	472442	SRX21346683	SRS18591743	SRA1691311	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.873		0.27005		0.75122		0.5172		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25132	25132	SRR25619752	SRX21346683	SRS18591743	SRP454714	PRJNA1004663	Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival	GSE240721	Other	Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach we demonstrate that larval RBs in zebrafish fall into three largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib which is used in clinic and causes peripheral neuropathy. Importantly dovitinib mediated axon loss can be suppressed by loss of Sarm1 a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solu…				30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	GSM7708237		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM7708237	GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq; Danio rerio; RNA Seq	GSM7708237 r1	GSM7708237	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454714		loader:fastq load.py	CEL201106AN_WT-2_S17_L004_I1_001.fastq.gz CEL201106AN_WT-2_S17_L004_R1_001.fastq.gz CEL201106AN_WT-2_S17_L004_R2_001.fastq.gz	fastq fastq fastq	14874414752.0	117121376.0	GSM7708237 r4	0:8 1:28 2:91	A:3301539475;C:2111151786;G:2317995421;T:2926865071;N:493463	8	28	91	3301539475	2111151786	2317995421	2926865071	493463	SRX21346683	SRS18591743	SRA1691311	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.87465		0.26977		0.75211		0.51651		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30012	30012	SRR28164886	SRX23795142	SRS20618185	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing CMO	scRNA seq wild type and hamp / 36 hpf CMO	Zebrafish embryo scRNA seq wild type and hamp / 36 hpf CMO		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf CMO\|dev stage:36 hpf CMO\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 36 hpf CMO	C 3	C 3	10x Genomics multiplexing CMO		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			36h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 36h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz	fastq fastq	42856660500.0	142855535.0	36h Multiplexing Capture S1 L001 R1 001.fastq.gz	0:150 1:150	A:8992350191;C:10354632010;G:13923089582;T:9585439035;N:1149682	150	150		8992350191	10354632010	13923089582	9585439035	1149682	SRX23795142	SRS20618185	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.0	0.0	0.0	0.0	1.0	1.0			150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30013	30013	SRR28164887	SRX23795141	SRS20618186	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing CMO	scRNA seq wild type and hamp / 24 hpf CMO	Zebrafish embryo scRNA seq wild type and hamp / 24 hpf CMO		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf CMO\|dev stage:24 hpf CMO\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 24 hpf CMO	C 2	C 2	10x Genomics multiplexing CMO		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			24h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 24h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz	fastq fastq	45212181900.0	150707273.0	24h Multiplexing Capture S1 L001 R1 001.fastq.gz	0:150 1:150	A:9741878752;C:11183590476;G:14447932886;T:9837582173;N:1197613	150	150		9741878752	11183590476	14447932886	9837582173	1197613	SRX23795141	SRS20618186	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.0	0.0	0.0	0.0	1.0	1.0			150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30014	30014	SRR28164888	SRX23795140	SRS20618184	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing CMO	scRNA seq wild type and hamp / 12 hpf CMO	Zebrafish embryo scRNA seq wild type and hamp / 12 hpf CMO		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf CMO\|dev stage:12 hpf CMO\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 12 hpf CMO	C 1	C 1	10x Genomics multiplexing CMO		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			12h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 12h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz	fastq fastq	23801259900.0	79337533.0	12h Multiplexing Capture S1 L001 R1 001.fastq.gz	0:150 1:150	A:5110000752;C:5818733743;G:7758205963;T:5113684708;N:634734	150	150		5110000752	5818733743	7758205963	5113684708	634734	SRX23795140	SRS20618184	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.0	0.0	0.0	0.0	1.0	1.0			150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
30015	30015	SRR28164889	SRX23795139	SRS20618183	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing GEX	scRNA seq wild type and hamp / 36 hpf GEX	Zebrafish embryo scRNA seq wild type and hamp / 36 hpf GEX		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf GEX\|dev stage:36 hpf GEX\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 36 hpf GEX	G 3	G 3	10x Genomics multiplexing GEX		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			36h_Gene_Expression_S1_L001_R2_001.fastq.gz 36h_Gene_Expression_S1_L001_R1_001.fastq.gz	fastq fastq	140285088600.0	467616962.0	36h Gene Expression S1 L001 R1 001.fastq.gz	0:150 1:150	A:41651884464;C:24916307056;G:25991077208;T:47722140024;N:3679848	150	150		41651884464	24916307056	25991077208	47722140024	3679848	SRX23795139	SRS20618183	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.00148	0.91873	0.0	0.15509	0.99985	0.78086	0.57142	0.52919	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30016	30016	SRR28164890	SRX23795138	SRS20618182	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing GEX	scRNA seq wild type and hamp / 24 hpf GEX	Zebrafish embryo scRNA seq wild type and hamp / 24 hpf GEX		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf GEX\|dev stage:24 hpf GEX\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 24 hpf GEX	G 2	G 2	10x Genomics multiplexing GEX		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			24h_Gene_Expression_S1_L001_R1_001.fastq.gz 24h_Gene_Expression_S1_L001_R2_001.fastq.gz	fastq fastq	147407645100.0	491358817.0	24h Gene Expression S1 L001 R1 001.fastq.gz	0:150 1:150	A:43802123106;C:26617386219;G:27720887375;T:49263400239;N:3848161	150	150		43802123106	26617386219	27720887375	49263400239	3848161	SRX23795138	SRS20618182	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.00129	0.92038	0.00042	0.15021	0.99993	0.77581	0.33333	0.51584	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30017	30017	SRR28164891	SRX23795137	SRS20618181	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing GEX	scRNA seq wild type and hamp / 12 hpf GEX	Zebrafish embryo scRNA seq wild type and hamp / 12 hpf GEX		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf GEX\|dev stage:12 hpf GEX\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 12 hpf GEX	G 1	G 1	10x Genomics multiplexing GEX		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			12h_Gene_Expression_S1_L001_R2_001.fastq.gz 12h_Gene_Expression_S1_L001_R1_001.fastq.gz	fastq fastq	204426398700.0	681421329.0	12h Gene Expression S1 L001 R1 001.fastq.gz	0:150 1:150	A:61302872939;C:35072603645;G:37153666376;T:70891933893;N:5321847	150	150		61302872939	35072603645	37153666376	70891933893	5321847	SRX23795137	SRS20618181	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.00085	0.9058	0.0	0.12081	0.99991	0.80231	0.5	0.52456	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31872	31872	SRR28764740	SRX24330059	SRS21091017	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 48h	GSM8222580		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:48 hpf loc name:missing\|collection date:missing	CEL210312AN WT 48h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:48 hpf	GSM8222580	GSM8222580: CEL210312AN WT 48h; Danio rerio; RNA Seq	GSM8222580 r1	GSM8222580	1	Forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_48h_S100_L003_I1_001.fastq.gz CEL210312AN_WT_48h_S100_L003_R1_001.fastq.gz CEL210312AN_WT_48h_S100_L003_R2_001.fastq.gz	fastq fastq fastq	8597674702.0	67698226.0	GSM8222580 r1	0:8 1:28 2:91	A:1824246454;C:1278127991;G:1448333280;T:1609791598;N:39243	8	28	91	1824246454	1278127991	1448333280	1609791598	39243	SRX24330059	SRS21091017	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Hatching	Embryo	Embryo Imprecise	All anatomical structures
31873	31873	SRR28764741	SRX24330059	SRS21091017	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 48h	GSM8222580		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:48 hpf loc name:missing\|collection date:missing	CEL210312AN WT 48h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:48 hpf	GSM8222580	GSM8222580: CEL210312AN WT 48h; Danio rerio; RNA Seq	GSM8222580 r1	GSM8222580	1	Forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_48h_S101_L003_I1_001.fastq.gz CEL210312AN_WT_48h_S101_L003_R1_001.fastq.gz CEL210312AN_WT_48h_S101_L003_R2_001.fastq.gz	fastq fastq fastq	10521686856.0	82847928.0	GSM8222580 r2	0:8 1:28 2:91	A:2230570510;C:1564859730;G:1774018840;T:1969664072;N:48296	8	28	91	2230570510	1564859730	1774018840	1969664072	48296	SRX24330059	SRS21091017	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Hatching	Embryo	Embryo Imprecise	All anatomical structures
31874	31874	SRR28764742	SRX24330059	SRS21091017	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 48h	GSM8222580		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:48 hpf loc name:missing\|collection date:missing	CEL210312AN WT 48h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:48 hpf	GSM8222580	GSM8222580: CEL210312AN WT 48h; Danio rerio; RNA Seq	GSM8222580 r1	GSM8222580	1	Forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_48h_S102_L003_I1_001.fastq.gz CEL210312AN_WT_48h_S102_L003_R1_001.fastq.gz CEL210312AN_WT_48h_S102_L003_R2_001.fastq.gz	fastq fastq fastq	10393048429.0	81835027.0	GSM8222580 r3	0:8 1:28 2:91	A:2205422432;C:1544223539;G:1750760277;T:1946533138;N:48071	8	28	91	2205422432	1544223539	1750760277	1946533138	48071	SRX24330059	SRS21091017	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Hatching	Embryo	Embryo Imprecise	All anatomical structures
31875	31875	SRR28764743	SRX24330059	SRS21091017	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 48h	GSM8222580		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:48 hpf loc name:missing\|collection date:missing	CEL210312AN WT 48h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:48 hpf	GSM8222580	GSM8222580: CEL210312AN WT 48h; Danio rerio; RNA Seq	GSM8222580 r1	GSM8222580	1	Forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_48h_S103_L003_I1_001.fastq.gz CEL210312AN_WT_48h_S103_L003_R1_001.fastq.gz CEL210312AN_WT_48h_S103_L003_R2_001.fastq.gz	fastq fastq fastq	1539235301.0	12119963.0	GSM8222580 r4	0:8 1:28 2:91	A:326058980;C:228846142;G:262343444;T:285660694;N:7373	8	28	91	326058980	228846142	262343444	285660694	7373	SRX24330059	SRS21091017	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Hatching	Embryo	Embryo Imprecise	All anatomical structures
31876	31876	SRR28764744	SRX24330058	SRS21091016	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 22h	GSM8222579		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:22 hpf loc name:missing\|collection date:missing	CEL210312AN WT 22h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:22 hpf	GSM8222579	GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq	GSM8222579 r1	GSM8222579	1	Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_22h_S96_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S96_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S96_L003_R2_001.fastq.gz	fastq fastq fastq	9045377769.0	71223447.0	GSM8222579 r1	0:8 1:28 2:91	A:1910521348;C:1357874019;G:1521970464;T:1690926373;N:41473	8	28	91	1910521348	1357874019	1521970464	1690926373	41473	SRX24330058	SRS21091016	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31877	31877	SRR28764745	SRX24330058	SRS21091016	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 22h	GSM8222579		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:22 hpf loc name:missing\|collection date:missing	CEL210312AN WT 22h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:22 hpf	GSM8222579	GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq	GSM8222579 r1	GSM8222579	1	Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_22h_S97_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S97_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S97_L003_R2_001.fastq.gz	fastq fastq fastq	9556753429.0	75250027.0	GSM8222579 r2	0:8 1:28 2:91	A:2016694527;C:1436202913;G:1608693558;T:1786117733;N:43726	8	28	91	2016694527	1436202913	1608693558	1786117733	43726	SRX24330058	SRS21091016	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31878	31878	SRR28764746	SRX24330058	SRS21091016	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 22h	GSM8222579		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:22 hpf loc name:missing\|collection date:missing	CEL210312AN WT 22h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:22 hpf	GSM8222579	GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq	GSM8222579 r1	GSM8222579	1	Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_22h_S98_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S98_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S98_L003_R2_001.fastq.gz	fastq fastq fastq	6838295188.0	53844844.0	GSM8222579 r3	0:8 1:28 2:91	A:1443225941;C:1028068269;G:1151922277;T:1276632644;N:31673	8	28	91	1443225941	1028068269	1151922277	1276632644	31673	SRX24330058	SRS21091016	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31879	31879	SRR28764747	SRX24330058	SRS21091016	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 22h	GSM8222579		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:22 hpf loc name:missing\|collection date:missing	CEL210312AN WT 22h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:22 hpf	GSM8222579	GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq	GSM8222579 r1	GSM8222579	1	Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_22h_S99_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S99_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S99_L003_R2_001.fastq.gz	fastq fastq fastq	8872634401.0	69863263.0	GSM8222579 r4	0:8 1:28 2:91	A:1873119195;C:1332238982;G:1493221194;T:1658936897;N:40665	8	28	91	1873119195	1332238982	1493221194	1658936897	40665	SRX24330058	SRS21091016	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31880	31880	SRR28738013	SRX24303940	SRS21066774	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 14h	GSM8216056		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:14 hpf loc name:missing\|collection date:missing	CEL210312AN WT 14h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:14 hpf	GSM8216056	GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq	GSM8216056 r1	GSM8216056	1	Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_14h_S92_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S92_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S92_L003_R2_001.fastq.gz	fastq fastq fastq	5909782440.0	46533720.0	GSM8216056 r1	0:8 1:28 2:91	A:1195361841;C:933687818;G:1057254177;T:1048237872;N:26812	8	28	91	1195361841	933687818	1057254177	1048237872	26812	SRX24303940	SRS21066774	SRA1848682	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31881	31881	SRR28738014	SRX24303940	SRS21066774	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 14h	GSM8216056		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:14 hpf loc name:missing\|collection date:missing	CEL210312AN WT 14h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:14 hpf	GSM8216056	GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq	GSM8216056 r1	GSM8216056	1	Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_14h_S93_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S93_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S93_L003_R2_001.fastq.gz	fastq fastq fastq	6519796333.0	51336979.0	GSM8216056 r2	0:8 1:28 2:91	A:1320007258;C:1029906863;G:1166350676;T:1155370144;N:30148	8	28	91	1320007258	1029906863	1166350676	1155370144	30148	SRX24303940	SRS21066774	SRA1848682	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31882	31882	SRR28738015	SRX24303940	SRS21066774	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 14h	GSM8216056		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:14 hpf loc name:missing\|collection date:missing	CEL210312AN WT 14h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:14 hpf	GSM8216056	GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq	GSM8216056 r1	GSM8216056	1	Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_14h_S94_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S94_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S94_L003_R2_001.fastq.gz	fastq fastq fastq	6288014983.0	49511929.0	GSM8216056 r3	0:8 1:28 2:91	A:1273032152;C:992961980;G:1124384567;T:1115177910;N:28930	8	28	91	1273032152	992961980	1124384567	1115177910	28930	SRX24303940	SRS21066774	SRA1848682	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31883	31883	SRR28738016	SRX24303940	SRS21066774	SRP502657	PRJNA1101966	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling	GSE264323	Transcriptome Analysis	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 7…				CEL210312AN WT 14h	GSM8216056		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:14 hpf loc name:missing\|collection date:missing	CEL210312AN WT 14h	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:14 hpf	GSM8216056	GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq	GSM8216056 r1	GSM8216056	1	Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657		loader:fastq load.py	CEL210312AN_WT_14h_S95_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S95_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S95_L003_R2_001.fastq.gz	fastq fastq fastq	6986621409.0	55012767.0	GSM8216056 r4	0:8 1:28 2:91	A:1412426673;C:1104618149;G:1250890162;T:1238194657;N:32156	8	28	91	1412426673	1104618149	1250890162	1238194657	32156	SRX24303940	SRS21066774	SRA1848682	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31972	31972	SRR28854385	SRX24414680	SRS21169984	SRP505049	PRJNA1106549	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling WT 30 h	GSE266312	Other	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…				scRNAseq	GSM8244692		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM8244692	GSM8244692: scRNAseq; Danio rerio; RNA Seq	GSM8244692 r1	GSM8244692	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049		loader:fastq load.py	CEL200616AN_WT_30h_S4_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S4_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S4_L001_R2_001.fastq.gz	fastq fastq fastq	5724917176.0	45078088.0	GSM8244692 r1	0:8 1:28 2:91	A:1233470398;C:840754101;G:925102747;T:1102656199;N:122563	8	28	91	1233470398	840754101	925102747	1102656199	122563	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31973	31973	SRR28854386	SRX24414680	SRS21169984	SRP505049	PRJNA1106549	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling WT 30 h	GSE266312	Other	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…				scRNAseq	GSM8244692		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM8244692	GSM8244692: scRNAseq; Danio rerio; RNA Seq	GSM8244692 r1	GSM8244692	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049		loader:fastq load.py	CEL200616AN_WT_30h_S4_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S4_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S4_L002_R2_001.fastq.gz	fastq fastq fastq	5783895468.0	45542484.0	GSM8244692 r2	0:8 1:28 2:91	A:1245735118;C:849017838;G:935656364;T:1113856043;N:100681	8	28	91	1245735118	849017838	935656364	1113856043	100681	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31974	31974	SRR28854387	SRX24414680	SRS21169984	SRP505049	PRJNA1106549	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling WT 30 h	GSE266312	Other	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…				scRNAseq	GSM8244692		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM8244692	GSM8244692: scRNAseq; Danio rerio; RNA Seq	GSM8244692 r1	GSM8244692	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049		loader:fastq load.py	CEL200616AN_WT_30h_S3_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S3_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S3_L001_R2_001.fastq.gz	fastq fastq fastq	6548658861.0	51564243.0	GSM8244692 r3	0:8 1:28 2:91	A:1411724640;C:961558289;G:1057832581;T:1261091330;N:139273	8	28	91	1411724640	961558289	1057832581	1261091330	139273	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31975	31975	SRR28854388	SRX24414680	SRS21169984	SRP505049	PRJNA1106549	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling WT 30 h	GSE266312	Other	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…				scRNAseq	GSM8244692		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM8244692	GSM8244692: scRNAseq; Danio rerio; RNA Seq	GSM8244692 r1	GSM8244692	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049		loader:fastq load.py	CEL200616AN_WT_30h_S3_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S3_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S3_L002_R2_001.fastq.gz	fastq fastq fastq	6602135640.0	51985320.0	GSM8244692 r4	0:8 1:28 2:91	A:1422617276;C:968975306;G:1067723068;T:1271232295;N:116175	8	28	91	1422617276	968975306	1067723068	1271232295	116175	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31976	31976	SRR28854389	SRX24414680	SRS21169984	SRP505049	PRJNA1106549	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling WT 30 h	GSE266312	Other	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…				scRNAseq	GSM8244692		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM8244692	GSM8244692: scRNAseq; Danio rerio; RNA Seq	GSM8244692 r1	GSM8244692	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049		loader:fastq load.py	CEL200616AN_WT_30h_S2_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S2_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S2_L001_R2_001.fastq.gz	fastq fastq fastq	5207105156.0	41000828.0	GSM8244692 r5	0:8 1:28 2:91	A:1121297258;C:765571677;G:841433529;T:1002663097;N:109787	8	28	91	1121297258	765571677	841433529	1002663097	109787	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31977	31977	SRR28854390	SRX24414680	SRS21169984	SRP505049	PRJNA1106549	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling WT 30 h	GSE266312	Other	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…				scRNAseq	GSM8244692		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM8244692	GSM8244692: scRNAseq; Danio rerio; RNA Seq	GSM8244692 r1	GSM8244692	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049		loader:fastq load.py	CEL200616AN_WT_30h_S2_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S2_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S2_L002_R2_001.fastq.gz	fastq fastq fastq	5257051208.0	41394104.0	GSM8244692 r6	0:8 1:28 2:91	A:1131659183;C:772616863;G:850242289;T:1012253749;N:91380	8	28	91	1131659183	772616863	850242289	1012253749	91380	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31978	31978	SRR28854391	SRX24414680	SRS21169984	SRP505049	PRJNA1106549	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling WT 30 h	GSE266312	Other	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…				scRNAseq	GSM8244692		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM8244692	GSM8244692: scRNAseq; Danio rerio; RNA Seq	GSM8244692 r1	GSM8244692	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049		loader:fastq load.py	CEL200616AN_WT_30h_S1_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S1_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S1_L001_R2_001.fastq.gz	fastq fastq fastq	5671346544.0	44656272.0	GSM8244692 r7	0:8 1:28 2:91	A:1221772454;C:832992882;G:915744544;T:1093089728;N:121144	8	28	91	1221772454	832992882	915744544	1093089728	121144	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31979	31979	SRR28854392	SRX24414680	SRS21169984	SRP505049	PRJNA1106549	Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling WT 30 h	GSE266312	Other	During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…				scRNAseq	GSM8244692		source name:zebrafish embryo\|cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf loc name:missing\|collection date:missing	scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo		Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neuron\|tissue:zebrafish embryo\|strain:mixed\|age:30 hpf	GSM8244692	GSM8244692: scRNAseq; Danio rerio; RNA Seq	GSM8244692 r1	GSM8244692	1	Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049		loader:fastq load.py	CEL200616AN_WT_30h_S1_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S1_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S1_L002_R2_001.fastq.gz	fastq fastq fastq	5728522071.0	45106473.0	GSM8244692 r8	0:8 1:28 2:91	A:1233691562;C:840924973;G:926085790;T:1103887111;N:99607	8	28	91	1233691562	840924973	926085790	1103887111	99607	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
32783	32783	SRR29438460	SRX24951082	SRS21654793	SRP514388	PRJNA1124950	Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution	GSE270075	Transcriptome Analysis	The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied with a focus on oxidative stress and inflammatory responses. However this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally heme synthesis was impaired leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.		pubmed:39846194		Zebra PS	GSM8334032		source name:embryos\|tissue:embryos\|Stage:120 hpf\|treatment:PS20nm exposure\|geo loc name:missing\|collection date:missing	Zebra PS	First the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104 and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene per barcode. Also clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv features.tsv matrix.mtx	embryos		The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer’s guidelines. Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.		tissue:embryos\|Stage:120 hpf\|treatment:PS20nm exposure	GSM8334032	GSM8334032: Zebra PS; Danio rerio; RNA Seq	GSM8334032 r1	GSM8334032	1	The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP514388			Zebra_PS_S1_L003_R2_001.fastq.gz Zebra_PS_S1_L003_R1_001.fastq.gz	fastq fastq	46515993156.0	400999941.0	GSM8334032 r1	0:26 1:90	A:10540890310;C:12256097063;G:11432529211;T:12270960287;N:15516285	26	90		10540890310	12256097063	11432529211	12270960287	15516285	SRX24951082	SRS21654793	SRA1904713	Pusan National University	Pusan National University	2	0.07013	0.96133	0.0269	0.15067	0.98135	0.78849	0.31441	0.54509	26	90	T	B	sc-like readlen	illumina	hiseq_era	5prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	South Korea	2024-06-17	Larval	Larval	Embryo Imprecise	All anatomical structures
32784	32784	SRR29438461	SRX24951081	SRS21654792	SRP514388	PRJNA1124950	Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution	GSE270075	Transcriptome Analysis	The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied with a focus on oxidative stress and inflammatory responses. However this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally heme synthesis was impaired leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.		pubmed:39846194		Zebra Control	GSM8334031		source name:embryos\|tissue:embryos\|Stage:120 hpf\|treatment:Wild type\|geo loc name:missing\|collection date:missing	Zebra Control	First the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104 and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene per barcode. Also clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv features.tsv matrix.mtx	embryos		The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer’s guidelines. Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.		tissue:embryos\|Stage:120 hpf\|treatment:Wild type	GSM8334031	GSM8334031: Zebra Control; Danio rerio; RNA Seq	GSM8334031 r1	GSM8334031	1	The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP514388			Zebra_Control_S1_L002_R1_001.fastq.gz Zebra_Control_S1_L002_R2_001.fastq.gz	fastq fastq	44451768632.0	383204902.0	GSM8334031 r1	0:26 1:90	A:10119968829;C:11732695259;G:10981098564;T:11603155786;N:14850194	26	90		10119968829	11732695259	10981098564	11603155786	14850194	SRX24951081	SRS21654792	SRA1904713	Pusan National University	Pusan National University	2	0.07283	0.96543	0.02838	0.15165	0.98052	0.78464	0.32149	0.56384	26	90	T	B	sc-like readlen	illumina	hiseq_era	5prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	South Korea	2024-06-17	Larval	Larval	Embryo Imprecise	All anatomical structures
33008	33008	SRR29632270	SRX25138332	SRS21830414	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 24h	GSM8366755		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 24h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366755	GSM8366755: Bmp4 explant 24h; Danio rerio; RNA Seq	GSM8366755 r1	GSM8366755	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4_24h_S1_L001_R1_001.fastq.gz Bmp4_24h_S1_L001_R2_001.fastq.gz	fastq fastq	49098784294.0	412594826.0	GSM8366755 r1	0:28 1:91	A:13643133254;C:11126085942;G:11676909916;T:12651522663;N:1132519	28	91		13643133254	11126085942	11676909916	12651522663	1132519	SRX25138332	SRS21830414	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33009	33009	SRR29632271	SRX25138331	SRS21830413	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 18h	GSM8366754		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 18h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366754	GSM8366754: Bmp4 explant 18h; Danio rerio; RNA Seq	GSM8366754 r1	GSM8366754	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4_18h_S1_L001_R1_001.fastq.gz Bmp4_18h_S1_L001_R2_001.fastq.gz	fastq fastq	44863080801.0	377000679.0	GSM8366754 r1	0:28 1:91	A:12441486571;C:10199111519;G:10790306255;T:11430847129;N:1329327	28	91		12441486571	10199111519	10790306255	11430847129	1329327	SRX25138331	SRS21830413	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33010	33010	SRR29632272	SRX25138330	SRS21830412	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 12h	GSM8366753		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 12h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366753	GSM8366753: Bmp4 explant 12h; Danio rerio; RNA Seq	GSM8366753 r1	GSM8366753	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4_12h_S1_L001_R1_001.fastq.gz Bmp4_12h_S1_L001_R2_001.fastq.gz	fastq fastq	50138128747.0	421328813.0	GSM8366753 r1	0:28 1:91	A:14089229753;C:10936347905;G:11403388741;T:13708020723;N:1141625	28	91		14089229753	10936347905	11403388741	13708020723	1141625	SRX25138330	SRS21830412	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33011	33011	SRR29632273	SRX25138329	SRS21830410	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 10h	GSM8366752		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 10h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366752	GSM8366752: Bmp4 explant 10h; Danio rerio; RNA Seq	GSM8366752 r1	GSM8366752	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4-10h_S1_L001_R1_001.fastq.gz Bmp4-10h_S1_L001_R2_001.fastq.gz	fastq fastq	149164547700.0	497215159.0	GSM8366752 r1	0:150 1:150	A:44020073879;C:31344780625;G:29505876494;T:44289819189;N:3997513	150	150		44020073879	31344780625	29505876494	44289819189	3997513	SRX25138329	SRS21830410	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33012	33012	SRR29632274	SRX25138328	SRS21830409	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 8h	GSM8366751		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 8h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366751	GSM8366751: Bmp4 explant 8h; Danio rerio; RNA Seq	GSM8366751 r1	GSM8366751	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4-8h_S1_L001_R1_001.fastq.gz Bmp4-8h_S1_L001_R2_001.fastq.gz	fastq fastq	118709118600.0	395697062.0	GSM8366751 r1	0:150 1:150	A:35474636770;C:23305712896;G:22894585568;T:37031410017;N:2773349	150	150		35474636770	23305712896	22894585568	37031410017	2773349	SRX25138328	SRS21830409	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33013	33013	SRR29632275	SRX25138327	SRS21830411	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 6h	GSM8366750		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 6h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366750	GSM8366750: Bmp4 explant 6h; Danio rerio; RNA Seq	GSM8366750 r1	GSM8366750	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4_6h_S1_L001_R1_001.fastq.gz Bmp4_6h_S1_L001_R2_001.fastq.gz	fastq fastq	52586645972.0	441904588.0	GSM8366750 r1	0:28 1:91	A:14755432217;C:11271293276;G:11858476334;T:14700289448;N:1154697	28	91		14755432217	11271293276	11858476334	14700289448	1154697	SRX25138327	SRS21830411	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	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");;