metadata: run_metadata: 402 rows where devstage_curation = "Pharyngula" and technology = "10x"

402 rows where devstage_curation = "Pharyngula" and technology = "10x"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_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
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
25133	25133	SRR25634296	SRX21361065	SRS18605555	SRP454944	PRJNA1005241	Nkx2.7 is a Conserved Regulator of Craniofacial Development	GSE240780	Transcriptome Analysis	Pharyngeal arch cells are comprised of endoderm mesoderm and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 / samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 / embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 / samples were pooled for submission.		pubmed:40268889		KC002 scRNAseq	GSM7709162		source name:Pharyngeal arches\|genotype:nkx2.7 / \|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf\|geo loc name:missing\|collection date:missing	KC002 scRNAseq	The read alignment and gene counting were made 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 version 105 Supplementary files format and content: Tab separated values files and matrix files	Pharyngeal arches		From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs 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 a sample index were added.		genotype:nkx2.7 / \|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf	GSM7709162	GSM7709162: KC002 scRNAseq; Danio rerio; RNA Seq	GSM7709162 r1	GSM7709162	1	From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs 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 a sample index we…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454944		loader:fastq load.py\|options: readTypes=TTBB read1PairFiles=KC002 S1 L004 I1 001.fastq.gz read2PairFiles=KC002 S1 L004 I2 001.fastq.gz read3PairFiles=KC002 S1 L004 R1 001.fastq.gz read4PairFiles=KC002 S1 L004 R2 001.fastq.gz	KC002_S1_L004_I1_001.fastq.gz KC002_S1_L004_I2_001.fastq.gz KC002_S1_L004_R1_001.fastq.gz KC002_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	65825988564.0	296513462.0	GSM7709162 r1	0:10 1:10 2:101 3:101	A:14990994149;C:11485312838;G:11921291570;T:21497933732;N:187035	10	10	101	101	14990994149	11485312838	11921291570	21497933732	187035	SRX21361065	SRS18605555	SRA1692494	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	2	0.00059	0.93473	2e-05	0.14487	0.99949	0.78364	0.5	0.52799	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Italy	2023-08-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
25134	25134	SRR25634297	SRX21361064	SRS18605556	SRP454944	PRJNA1005241	Nkx2.7 is a Conserved Regulator of Craniofacial Development	GSE240780	Transcriptome Analysis	Pharyngeal arch cells are comprised of endoderm mesoderm and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 / samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 / embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 / samples were pooled for submission.		pubmed:40268889		KC001 scRNAseq	GSM7709161		source name:Pharyngeal arches\|genotype:wild type\|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf\|geo loc name:missing\|collection date:missing	KC001 scRNAseq	The read alignment and gene counting were made 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 version 105 Supplementary files format and content: Tab separated values files and matrix files	Pharyngeal arches		From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs 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 a sample index were added.		genotype:wild type\|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf	GSM7709161	GSM7709161: KC001 scRNAseq; Danio rerio; RNA Seq	GSM7709161 r1	GSM7709161	1	From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs 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 a sample index we…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454944		loader:fastq load.py\|options: readTypes=TTBB read1PairFiles=KC001 S1 L004 I1 001.fastq.gz read2PairFiles=KC001 S1 L004 I2 001.fastq.gz read3PairFiles=KC001 S1 L004 R1 001.fastq.gz read4PairFiles=KC001 S1 L004 R2 001.fastq.gz	KC001_S1_L004_I1_001.fastq.gz KC001_S1_L004_I2_001.fastq.gz KC001_S1_L004_R1_001.fastq.gz KC001_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	69380677872.0	312525576.0	GSM7709161 r1	0:10 1:10 2:101 3:101	A:16018222868;C:11704492905;G:12161620273;T:23245625739;N:204567	10	10	101	101	16018222868	11704492905	12161620273	23245625739	204567	SRX21361064	SRS18605556	SRA1692494	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	2	0.00071	0.93976	0.0001	0.12725	0.99945	0.78457	0.75	0.50121	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Italy	2023-08-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
29808	29808	SRR27450807	SRX23122487	SRS20076037	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673		Zebrafish EC 24hpf Aktmutant	GSM8004755		source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf Aktmutant	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant	GSM8004755	GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq	GSM8004755 r1	GSM8004755	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328		loader:fastq load.py	mu1-23-19_DRT_S2_L001_I1_001.fastq.gz mu1-23-19_DRT_S2_L001_R1_001.fastq.gz mu1-23-19_DRT_S2_L001_R2_001.fastq.gz	fastq fastq fastq	23281472741.0	183318683.0	GSM8004755 r1	0:8 1:28 2:91	A:4703583066;C:3702175361;G:3998796644;T:4271932211;N:5512871	8	28	91		4703583066	3702175361	3998796644	4271932211	5512871	SRX23122487	SRS20076037	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29809	29809	SRR27450808	SRX23122487	SRS20076037	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673		Zebrafish EC 24hpf Aktmutant	GSM8004755		source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf Aktmutant	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant	GSM8004755	GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq	GSM8004755 r1	GSM8004755	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328		loader:fastq load.py	mu1-23-19_DRT_S2_L002_I1_001.fastq.gz mu1-23-19_DRT_S2_L002_R1_001.fastq.gz mu1-23-19_DRT_S2_L002_R2_001.fastq.gz	fastq fastq fastq	21009317138.0	165427694.0	GSM8004755 r2	0:8 1:28 2:91	A:4231955850;C:3363548064;G:3603913589;T:3849411287;N:5091364	8	28	91		4231955850	3363548064	3603913589	3849411287	5091364	SRX23122487	SRS20076037	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29810	29810	SRR27450809	SRX23122486	SRS20076036	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673		Zebrafish EC 24hpf WT	GSM8004754		source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf WT	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT	GSM8004754	GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq	GSM8004754 r1	GSM8004754	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328		loader:fastq load.py	wt1-23-19_DRT_S1_L001_I1_001.fastq.gz wt1-23-19_DRT_S1_L001_R1_001.fastq.gz wt1-23-19_DRT_S1_L001_R2_001.fastq.gz	fastq fastq fastq	22261273232.0	175285616.0	GSM8004754 r1	0:8 1:28 2:91	A:4475749188;C:3578353646;G:3836029871;T:4055646794;N:5211557	8	28	91		4475749188	3578353646	3836029871	4055646794	5211557	SRX23122486	SRS20076036	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29811	29811	SRR27450810	SRX23122486	SRS20076036	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673		Zebrafish EC 24hpf WT	GSM8004754		source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf WT	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT	GSM8004754	GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq	GSM8004754 r1	GSM8004754	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328		loader:fastq load.py	wt1-23-19_DRT_S1_L002_I1_001.fastq.gz wt1-23-19_DRT_S1_L002_R1_001.fastq.gz wt1-23-19_DRT_S1_L002_R2_001.fastq.gz	fastq fastq fastq	20084395188.0	158144844.0	GSM8004754 r2	0:8 1:28 2:91	A:4028678970;C:3250176957;G:3455600305;T:3651884457;N:4840115	8	28	91		4028678970	3250176957	3455600305	3651884457	4840115	SRX23122486	SRS20076036	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
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
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
31527	31527	SRR28419475	SRX24023798	SRS20818154	SRP497235	PRJNA1090867	Single cell RNA seq of zebrafish endothelial cells	GSE262232	Transcriptome Analysis	We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.		pubmed:39977018		Zebrafish endothelial cells 34 hpf	GSM8160885		source name:Whole body\|tissue:Whole body\|age:embryo\|geo loc name:missing\|collection date:missing	Zebrafish endothelial cells 34 hpf	Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files perform the alignment barcode counting and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files	Whole body		Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.		tissue:Whole body\|age:embryo	GSM8160885	GSM8160885: Zebrafish endothelial cells 34 hpf; Danio rerio; RNA Seq	GSM8160885 r1	GSM8160885	1	Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP497235		assembly:GRCz11\|intentional duplicate\|dangling references:treat as unmapped\|dangling references:skip reference resolution	34hpf_possorted_genome_bam.bam	10X Genomics bam file	8518745844.0	86925978.0	GSM8160885 r1	0:98	A:2440648674;C:1828442217;G:2000096456;T:2232243146;N:17315351	98				2440648674	1828442217	2000096456	2232243146	17315351	SRX24023798	SRS20818154	SRA1835509	Uppsala University	Uppsala University	1	0.92268		0.1011		0.82235		0.50276		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Sweden	2024-03-22	Pharyngula	Embryo	Trunk	Surface Structure
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
33617	33617	SRR30274406	SRX25735496	SRS22375280	SRP526857	PRJNA1148965	The Gq/11 family of G alpha subunits is necessary and sufficient for lower jaw development	GSE275013	Transcriptome Analysis	Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A Ednra and secreted ligand Endothelin 1 Edn1. The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. As a first step towards addressing this question we examined the function of the Gq/11 family of Ga subunits in zebrafish using pharmacological and genetic ablation of Gq/11 activity and transgenic induction of a constitutively active Gq protein in edn1 / embryos. Loss of Gq/11 activity fully recapitulated the edn1 / phenotype with genes encoding for G11 being most essential. Furthermore inducing Gq activity in edn1 / embryos not only restored Ednra dependent jaw structures and gene expression signatures but also caused homeosis of the upper jaw structures into a lower jaw like structure. These results indicate that Gq/11 is necessary and sufficient to mediate the lower jaw patterning mechanism for Ednra. Overall design: Zebrafish embryos were first treated with YM 254890 or DMSO control between 16 36 hpf. Then cranial neural crest cells NCCs labeled with two transgenes sox10:mRFP and fli1a:EGFP were isolated at 36 hpf by fluorescence activated cell sorting FACS. Isolated cranial NCCs were then analyzed by scRNA seq.		pubmed:39345358;pubmed:40171762		cranial NCCs YM	GSM8464445		source name:Facial mesenchyme\|tissue:Facial mesenchyme\|age:36 hpf\|cell type:Cranial neural crest cells\|genotype:Tgsox10:mRFP;Tgfli1a:EGFP\|treatment:YM\|geo loc name:missing\|collection date:missing	cranial NCCs YM	Sequence reads were converted to count matrices with Cell Ranger v5.0.1 10X Genomics. Subsequent analyses of count matrices were performed with Seurat version 4.3.0 in R studio. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Facial mesenchyme	Dechorionated zebrafish embryos were treated with 100uM YM 254890 or 10%v/v DMSO vehicle control from 16 hpf 36 hpf	Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al. 2016; Askary et al. 2017; Mitchell et al. 2021 with some modifications. In brief 140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche cat. 10165921001 then 70 embryos were treated with 100 uM YM 254890 Adipogen cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf 10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos the heads were severed pooled and deyolked by gentle pipetting in Ca2+ free Ringer’s solution 116 mM NaCl 2.9 mM KCl 5 mM HEPES pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold activated protease from Bacillus licheniformis Sigma Aldrich cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease 125 U/ml DNAse 2.5 mM EDTA PBS followed by enzyme neutralization with stop solution 30% fetal bovine serum 0.8 mM CaCl2 in PBS. Cells were then centrifuged 400xg resuspended in cell suspension buffer [1% fetal bovine serum 0.8 mM CaCl2 Leibovitz’s L 15 Medium Gibco cat. 21083 027] filtered through a 70 uM strainer PluriSelect cat. 43 10040 40 centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum 1 mM EDTA 25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco cat. 15250 061 8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime Next…		tissue:Facial mesenchyme\|age:36 hpf\|cell type:Cranial neural crest cells\|genotype:Tgsox10:mRFP;Tgfli1a:EGFP\|treatment:YM	GSM8464445	GSM8464445: cranial NCCs YM; Danio rerio; RNA Seq	GSM8464445 r1	GSM8464445	1	Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al. 2016; Askary et al. 2017; Mitchell et al. 2021 with some modifications. In brief 140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche cat. 10165921001 then 70 embryos were treated with 100 uM YM 254890 Adipogen cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf 10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos the heads were severed pooled and deyolked by gentle pipetting in Ca2+ free Ringer's solution 116 mM NaCl 2.9 mM KCl 5 mM HEPES pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold activated protease from Bacillus licheniformis Sigma Aldrich cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease 125 U/ml DNAse 2.5 mM EDTA PBS followed by enzyme neutralization with stop solution 30% fetal bovine serum 0.8 mM CaCl2 in PBS. Cells were then centrifuged 400xg resuspended in cell suspension buffer [1% fetal bovine serum 0.8 mM CaCl2 Leibovitz's L 15 Medium Gibco cat. 21083 027] filtered through a 70 uM strainer PluriSelect cat. 43 10040 40 centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum 1 mM EDTA 25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco cat. 15250 061 8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime Next…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP526857			YM-treated_S9_L001_R2_001.fastq.gz YM-treated_S9_L001_R1_001.fastq.gz	fastq fastq	133560759038.0	442254169.0	GSM8464445 r1	0:151 1:151	A:49523643076;C:22144256343;G:30982866215;T:30893839980;N:16153424	151	151			49523643076	22144256343	30982866215	30893839980	16153424	SRX25735496	SRS22375280	SRA1949431	David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus	David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus	2	0.00156	0.3917	0.00133	0.06002	0.99997	0.9529	0.0	0.52259	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-16	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
33618	33618	SRR30274407	SRX25735495	SRS22375277	SRP526857	PRJNA1148965	The Gq/11 family of G alpha subunits is necessary and sufficient for lower jaw development	GSE275013	Transcriptome Analysis	Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A Ednra and secreted ligand Endothelin 1 Edn1. The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. As a first step towards addressing this question we examined the function of the Gq/11 family of Ga subunits in zebrafish using pharmacological and genetic ablation of Gq/11 activity and transgenic induction of a constitutively active Gq protein in edn1 / embryos. Loss of Gq/11 activity fully recapitulated the edn1 / phenotype with genes encoding for G11 being most essential. Furthermore inducing Gq activity in edn1 / embryos not only restored Ednra dependent jaw structures and gene expression signatures but also caused homeosis of the upper jaw structures into a lower jaw like structure. These results indicate that Gq/11 is necessary and sufficient to mediate the lower jaw patterning mechanism for Ednra. Overall design: Zebrafish embryos were first treated with YM 254890 or DMSO control between 16 36 hpf. Then cranial neural crest cells NCCs labeled with two transgenes sox10:mRFP and fli1a:EGFP were isolated at 36 hpf by fluorescence activated cell sorting FACS. Isolated cranial NCCs were then analyzed by scRNA seq.		pubmed:39345358;pubmed:40171762		cranial NCCs DMSO	GSM8464444		source name:Facial mesenchyme\|tissue:Facial mesenchyme\|age:36 hpf\|cell type:Cranial neural crest cells\|genotype:Tgsox10:mRFP;Tgfli1a:EGFP\|treatment:DMSO\|geo loc name:missing\|collection date:missing	cranial NCCs DMSO	Sequence reads were converted to count matrices with Cell Ranger v5.0.1 10X Genomics. Subsequent analyses of count matrices were performed with Seurat version 4.3.0 in R studio. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Facial mesenchyme	Dechorionated zebrafish embryos were treated with 100uM YM 254890 or 10%v/v DMSO vehicle control from 16 hpf 36 hpf	Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al. 2016; Askary et al. 2017; Mitchell et al. 2021 with some modifications. In brief 140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche cat. 10165921001 then 70 embryos were treated with 100 uM YM 254890 Adipogen cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf 10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos the heads were severed pooled and deyolked by gentle pipetting in Ca2+ free Ringer’s solution 116 mM NaCl 2.9 mM KCl 5 mM HEPES pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold activated protease from Bacillus licheniformis Sigma Aldrich cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease 125 U/ml DNAse 2.5 mM EDTA PBS followed by enzyme neutralization with stop solution 30% fetal bovine serum 0.8 mM CaCl2 in PBS. Cells were then centrifuged 400xg resuspended in cell suspension buffer [1% fetal bovine serum 0.8 mM CaCl2 Leibovitz’s L 15 Medium Gibco cat. 21083 027] filtered through a 70 uM strainer PluriSelect cat. 43 10040 40 centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum 1 mM EDTA 25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco cat. 15250 061 8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime Next…		tissue:Facial mesenchyme\|age:36 hpf\|cell type:Cranial neural crest cells\|genotype:Tgsox10:mRFP;Tgfli1a:EGFP\|treatment:DMSO	GSM8464444	GSM8464444: cranial NCCs DMSO; Danio rerio; RNA Seq	GSM8464444 r1	GSM8464444	1	Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al. 2016; Askary et al. 2017; Mitchell et al. 2021 with some modifications. In brief 140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche cat. 10165921001 then 70 embryos were treated with 100 uM YM 254890 Adipogen cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf 10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos the heads were severed pooled and deyolked by gentle pipetting in Ca2+ free Ringer's solution 116 mM NaCl 2.9 mM KCl 5 mM HEPES pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold activated protease from Bacillus licheniformis Sigma Aldrich cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease 125 U/ml DNAse 2.5 mM EDTA PBS followed by enzyme neutralization with stop solution 30% fetal bovine serum 0.8 mM CaCl2 in PBS. Cells were then centrifuged 400xg resuspended in cell suspension buffer [1% fetal bovine serum 0.8 mM CaCl2 Leibovitz's L 15 Medium Gibco cat. 21083 027] filtered through a 70 uM strainer PluriSelect cat. 43 10040 40 centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum 1 mM EDTA 25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco cat. 15250 061 8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime Next…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP526857			untreated_S8_L001_R2_001.fastq.gz untreated_S8_L001_R1_001.fastq.gz	fastq fastq	105068673228.0	347909514.0	GSM8464444 r1	0:151 1:151	A:37833743112;C:17968955370;G:25241339852;T:24012078661;N:12556233	151	151			37833743112	17968955370	25241339852	24012078661	12556233	SRX25735495	SRS22375277	SRA1949431	David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus	David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus	2	0.00043	0.49133	0.00042	0.07262	1.0	0.95179		0.5212	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-16	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
33892	33892	SRR30866052	SRX26263961	SRS22803217	SRP536276	PRJNA1168147	Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq]	GSE278654	Transcriptome Analysis	Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.				m4b mut	GSM8552316		tissue:melanocytes\|cell type:melanocytes\|age:36 hpf\|genotype:mgat4b mutant\|treatment:No\|geo loc name:missing\|collection date:missing	m4b mut	Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features and matrix files	melanocytes		The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction		cell type:melanocytes\|age:36 hpf\|genotype:mgat4b mutant\|treatment:No	GSM8552316	GSM8552316: m4b mut; Danio rerio; RNA Seq	GSM8552316 r1	GSM8552316	1	The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP536276		loader:fastq load.py	m4b_mut_S2_L001_I1_001.fastq.gz m4b_mut_S2_L001_I2_001.fastq.gz m4b_mut_S2_L001_R1_001.fastq.gz m4b_mut_S2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	18274385040.0	132423080.0	GSM8552316 r1	0:10 1:10 2:28 3:90	A:3788703303;C:2355223955;G:2645521958;T:3126630009;N:1997975	10	10	28	90	3788703303	2355223955	2645521958	3126630009	1997975	SRX26263961	SRS22803217	SRA1984944	Pigment Cell Biology Lab, CSIR-IGIB	Pigment Cell Biology Lab, CSIR-IGIB												B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2024-10-02	Pharyngula	Embryo	Skin	Surface Structure
33893	33893	SRR30866053	SRX26263960	SRS22803216	SRP536276	PRJNA1168147	Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq]	GSE278654	Transcriptome Analysis	Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.				Control	GSM8552315		tissue:melanocytes\|cell type:melanocytes\|age:36 hpf\|genotype:control\|treatment:No\|geo loc name:missing\|collection date:missing	Control	Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features and matrix files	melanocytes		The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction		cell type:melanocytes\|age:36 hpf\|genotype:control\|treatment:No	GSM8552315	GSM8552315: Control; Danio rerio; RNA Seq	GSM8552315 r1	GSM8552315	1	The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP536276		loader:fastq load.py	con_S1_L001_I1_001.fastq.gz con_S1_L001_I2_001.fastq.gz con_S1_L001_R1_001.fastq.gz con_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	15825218034.0	114675493.0	GSM8552315 r1	0:10 1:10 2:28 3:90	A:3074750870;C:2137365424;G:2401965854;T:2704984993;N:1727229	10	10	28	90	3074750870	2137365424	2401965854	2704984993	1727229	SRX26263960	SRS22803216	SRA1984944	Pigment Cell Biology Lab, CSIR-IGIB	Pigment Cell Biology Lab, CSIR-IGIB												B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2024-10-02	Pharyngula	Embryo	Skin	Surface Structure
35387	35387	SRR32649450	SRX27953869	SRS24319773	SRP569567	PRJNA1234533	Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb	GSE291626	Transcriptome Analysis	To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.				OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish	GSM8838716		source name:Olfactory Sensory Tissue\|tissue:Olfactory Sensory Tissue\|cell line:Olactory Sensory Neurons\|cell type:Neurons\|sample age:36 hpf\|genotype:Tgomp:lyn RFP\|geo loc name:missing\|collection date:missing	OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish	Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.	Olfactory Sensory Tissue		10X Genomics V3.3		tissue:Olfactory Sensory Tissue\|cell line:Olactory Sensory Neurons\|cell type:Neurons\|sample age:36 hpf\|genotype:Tgomp:lyn RFP	GSM8838716	GSM8838716: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish; Danio rerio; RNA Seq	GSM8838716 r1	GSM8838716	1	10X Genomics V3.3		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP569567		loader:fastq load.py	97366_S7_L001_I1_001.fastq.gz 97366_S7_L001_R1_001.fastq.gz 97366_S7_L001_R2_001.fastq.gz	fastq fastq fastq	5962313630.0	45863951.0	GSM8838716 r1	0:8 1:28 2:94	A:1285269727;C:856096209;G:931439088;T:1238303640;N:102730	8	28	94		1285269727	856096209	931439088	1238303640	102730	SRX27953869	SRS24319773	SRA2091725	Department of Neuroscience, University of Pennsylvania	Department of Neuroscience, University of Pennsylvania												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-11	Pharyngula	Embryo	Brain	Nervous System
35388	35388	SRR32649451	SRX27953869	SRS24319773	SRP569567	PRJNA1234533	Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb	GSE291626	Transcriptome Analysis	To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.				OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish	GSM8838716		source name:Olfactory Sensory Tissue\|tissue:Olfactory Sensory Tissue\|cell line:Olactory Sensory Neurons\|cell type:Neurons\|sample age:36 hpf\|genotype:Tgomp:lyn RFP\|geo loc name:missing\|collection date:missing	OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish	Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.	Olfactory Sensory Tissue		10X Genomics V3.3		tissue:Olfactory Sensory Tissue\|cell line:Olactory Sensory Neurons\|cell type:Neurons\|sample age:36 hpf\|genotype:Tgomp:lyn RFP	GSM8838716	GSM8838716: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish; Danio rerio; RNA Seq	GSM8838716 r1	GSM8838716	1	10X Genomics V3.3		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP569567		loader:fastq load.py	97366_S7_L002_I1_001.fastq.gz 97366_S7_L002_R1_001.fastq.gz 97366_S7_L002_R2_001.fastq.gz	fastq fastq fastq	5980615420.0	46004734.0	GSM8838716 r2	0:8 1:28 2:94	A:1289600464;C:857667521;G:934976316;T:1242064603;N:136092	8	28	94		1289600464	857667521	934976316	1242064603	136092	SRX27953869	SRS24319773	SRA2091725	Department of Neuroscience, University of Pennsylvania	Department of Neuroscience, University of Pennsylvania												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-11	Pharyngula	Embryo	Brain	Nervous System
50662	50662	SRR8206453	SRX5025778	SRS4057278	SRP169565	PRJNA506002	Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina	GSE122680	Transcriptome Analysis	It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage		pubmed:32467236		36 hpf retina	GSM3478014		source name:Retina\|strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:36 hpf	36 hpf retina	Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx	Retina		We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer’s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer’s protocol.		strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:36 hpf	GSM3478014	GSM3478014: 36 hpf retina; Danio rerio; RNA Seq	GSM3478014		1	We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.	GEO Accession:GSM3478014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP169565			36hpf_possorted_genome_bam.bam	10X Genomics bam file	55066871015.0	364681265.0	GSM3478014 r1	0:151	A:16004920970;C:11846723571;G:11830068402;T:15383410377;N:1747695	151				16004920970	11846723571	11830068402	15383410377	1747695	SRX5025778	SRS4057278	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.86264		0.06425		0.83834		0.48474		151		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Pharyngula	Embryo	Eye	Sensory System
50663	50663	SRR8206452	SRX5025777	SRS4057277	SRP169565	PRJNA506002	Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina	GSE122680	Transcriptome Analysis	It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage		pubmed:32467236		24 hpf retina	GSM3478013		source name:Retina\|strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:24 hpf	24 hpf retina	Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx	Retina		We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer’s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer’s protocol.		strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:24 hpf	GSM3478013	GSM3478013: 24 hpf retina; Danio rerio; RNA Seq	GSM3478013		1	We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.	GEO Accession:GSM3478013	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP169565			24hpf_possorted_genome_bam.bam	10X Genomics bam file	64649431883.0	428141933.0	GSM3478013 r1	0:151	A:18206375554;C:14387069686;G:14012075221;T:18041887869;N:2023553	151				18206375554	14387069686	14012075221	18041887869	2023553	SRX5025777	SRS4057277	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.88151		0.05606		0.8369		0.50733		151		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Pharyngula	Embryo	Eye	Sensory System
51190	51190	SRR8592250	SRX5392462	SRS4380285	SRP186305	PRJNA522917	Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation	GSE126647	Transcriptome Analysis	Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated few signals are understood that specifically restrict the size of the vertebrate OFT. Here we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants which lack the transcription factor Pbx4 produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors which contribute to the OFT and adjacent endothelial cell progenitors which contribute to posterior pharyngeal arch arteries. Subsequently Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior differentiated cardiomyocyte populations. Therefore the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes we utilized single cell RNA Seq scRNA Seq data sets collected from control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.		pubmed:32094112		Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	GSM3610371		source name:Pbx4 depleted nkx2.5:ZsYellow+ cells\|strain background:AB/TU\|age:28 hpf depleted\|tissue:cardiac progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment filtering barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv Genes genes.tsv and Matrix matrix.mtx	Pbx4 depleted nkx2.5:ZsYellow+ cells		Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry		strain background:AB/TU\|age:28 hpf depleted\|tissue:cardiac progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	GSM3610371	GSM3610371: Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq	GSM3610371		1	Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry	GEO Accession:GSM3610371	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP186305		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=10X PBX4 mo injected 3zf S2 L001 I1 001.fastq.gz read2PairFiles=10X PBX4 mo injected 3zf S2 L001 R1 001.fastq.gz read3PairFiles=10X PBX4 mo injected 3zf S2 L001 R2 001.fastq.gz	10X_PBX4_mo_injected_3zf_S2_L001_I1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L001_R1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L001_R2_001.fastq.gz	fastq fastq fastq	13771731610.0	75668855.0	GSM3610371 r1	0:8 1:27 2:147	A:3868981340;C:3004344480;G:3173242889;T:3705905113;N:19257788	8	27	147		3868981340	3004344480	3173242889	3705905113	19257788	SRX5392462	SRS4380285	SRA850447	GEO	Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital	1	0.91532		0.07049		0.82722		0.50962		147		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-02-15	Pharyngula	Embryo	Heart	Cardiovascular System
51191	51191	SRR8592251	SRX5392462	SRS4380285	SRP186305	PRJNA522917	Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation	GSE126647	Transcriptome Analysis	Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated few signals are understood that specifically restrict the size of the vertebrate OFT. Here we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants which lack the transcription factor Pbx4 produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors which contribute to the OFT and adjacent endothelial cell progenitors which contribute to posterior pharyngeal arch arteries. Subsequently Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior differentiated cardiomyocyte populations. Therefore the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes we utilized single cell RNA Seq scRNA Seq data sets collected from control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.		pubmed:32094112		Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	GSM3610371		source name:Pbx4 depleted nkx2.5:ZsYellow+ cells\|strain background:AB/TU\|age:28 hpf depleted\|tissue:cardiac progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment filtering barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv Genes genes.tsv and Matrix matrix.mtx	Pbx4 depleted nkx2.5:ZsYellow+ cells		Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry		strain background:AB/TU\|age:28 hpf depleted\|tissue:cardiac progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	GSM3610371	GSM3610371: Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq	GSM3610371		1	Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry	GEO Accession:GSM3610371	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP186305		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=10X PBX4 mo injected 3zf S2 L002 I1 001.fastq.gz read2PairFiles=10X PBX4 mo injected 3zf S2 L002 R1 001.fastq.gz read3PairFiles=10X PBX4 mo injected 3zf S2 L002 R2 001.fastq.gz	10X_PBX4_mo_injected_3zf_S2_L002_I1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L002_R1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L002_R2_001.fastq.gz	fastq fastq fastq	13960104704.0	76703872.0	GSM3610371 r2	0:8 1:27 2:147	A:3921736827;C:3045954411;G:3216708567;T:3758217760;N:17487139	8	27	147		3921736827	3045954411	3216708567	3758217760	17487139	SRX5392462	SRS4380285	SRA850447	GEO	Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital	1	0.91469		0.06915		0.82747		0.49959		147		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-02-15	Pharyngula	Embryo	Heart	Cardiovascular System
51192	51192	SRR8592248	SRX5392461	SRS4380284	SRP186305	PRJNA522917	Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation	GSE126647	Transcriptome Analysis	Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated few signals are understood that specifically restrict the size of the vertebrate OFT. Here we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants which lack the transcription factor Pbx4 produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors which contribute to the OFT and adjacent endothelial cell progenitors which contribute to posterior pharyngeal arch arteries. Subsequently Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior differentiated cardiomyocyte populations. Therefore the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes we utilized single cell RNA Seq scRNA Seq data sets collected from control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.		pubmed:32094112		control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	GSM3610370		tissue:control nkx2.5:ZsYellow+ cells\|strain background:AB/TU\|age:28 hpf progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment filtering barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv Genes genes.tsv and Matrix matrix.mtx	control nkx2.5:ZsYellow+ cells		Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry		strain background:AB/TU\|age:28 hpf progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	GSM3610370	GSM3610370: control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq	GSM3610370		1	Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry	GEO Accession:GSM3610370	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP186305		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=10X Ctrl uninjected 3zf S1 L001 I1 001.fastq.gz read2PairFiles=10X Ctrl uninjected 3zf S1 L001 R1 001.fastq.gz read3PairFiles=10X Ctrl uninjected 3zf S1 L001 R2 001.fastq.gz	10X_Ctrl_uninjected_3zf_S1_L001_I1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L001_R1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L001_R2_001.fastq.gz	fastq fastq fastq	13724509526.0	75409393.0	GSM3610370 r1	0:8 1:27 2:147	A:3850897681;C:3014748648;G:3154637947;T:3685016570;N:19208680	8	27	147		3850897681	3014748648	3154637947	3685016570	19208680	SRX5392461	SRS4380284	SRA850447	GEO	Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital	1	0.91575		0.07488		0.82871		0.51761		147		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-02-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
51193	51193	SRR8592249	SRX5392461	SRS4380284	SRP186305	PRJNA522917	Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation	GSE126647	Transcriptome Analysis	Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated few signals are understood that specifically restrict the size of the vertebrate OFT. Here we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants which lack the transcription factor Pbx4 produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors which contribute to the OFT and adjacent endothelial cell progenitors which contribute to posterior pharyngeal arch arteries. Subsequently Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior differentiated cardiomyocyte populations. Therefore the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes we utilized single cell RNA Seq scRNA Seq data sets collected from control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.		pubmed:32094112		control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	GSM3610370		tissue:control nkx2.5:ZsYellow+ cells\|strain background:AB/TU\|age:28 hpf progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment filtering barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv Genes genes.tsv and Matrix matrix.mtx	control nkx2.5:ZsYellow+ cells		Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry		strain background:AB/TU\|age:28 hpf progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	GSM3610370	GSM3610370: control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq	GSM3610370		1	Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry	GEO Accession:GSM3610370	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP186305		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=10X Ctrl uninjected 3zf S1 L002 I1 001.fastq.gz read2PairFiles=10X Ctrl uninjected 3zf S1 L002 R1 001.fastq.gz read3PairFiles=10X Ctrl uninjected 3zf S1 L002 R2 001.fastq.gz	10X_Ctrl_uninjected_3zf_S1_L002_I1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L002_R1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L002_R2_001.fastq.gz	fastq fastq fastq	13903413706.0	76392383.0	GSM3610370 r2	0:8 1:27 2:147	A:3900618364;C:3054470646;G:3195816893;T:3735199844;N:17307959	8	27	147		3900618364	3054470646	3195816893	3735199844	17307959	SRX5392461	SRS4380284	SRA850447	GEO	Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital	1	0.91438		0.07364		0.82893		0.50278		147		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-02-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
53001	53001	SRR12173589	SRX8688333	SRS6966994	SRP213938	PRJNA553572	A map of cis regulatory elements and 3D genome structures in zebrafish	GSE134055	Other	The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.		pubmed:33239788;pubmed:35649578		YueLab RNA seq Blood rep2	GSM4662086		source name:YueLab RNA seq Blood\|strain:Tuebingen\|tissue:Blood	YueLab RNA seq Blood rep2	RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac H3K4me3 ChIP seq were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain we called the peak using Homer with the parameter “ region size 1000” and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged	YueLab RNA seq Blood		RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext…	RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq ATAC seq Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions	strain:Tuebingen\|tissue:Blood	GSM4662086	GSM4662086: YueLab RNA seq Blood rep2; Danio rerio; RNA Seq	GSM4662086		1	RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext…	GEO Accession:GSM4662086	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP213938			YueLab-RNA-seq-Blood-rep2_2.fastq.gz YueLab-RNA-seq-Blood-rep2_1.fastq.gz	fastq fastq	9750305560.0	32285780.0	GSM4662086 r1	0:151 1:151	A:2564237490;C:2313022617;G:2328740350;T:2544206938;N:98165	151	151			2564237490	2313022617	2328740350	2544206938	98165	SRX8688333	SRS6966994	SRA919194	GEO	Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine	2	0.90976	0.90587	0.07014	0.06953	0.85415	0.85624	0.51898	0.51696	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	sc	single_cell_droplet	10x	United States	2020-07-08	Pharyngula	Embryo	Blood	Hematopoietic System
53002	53002	SRR12173588	SRX8688332	SRS6966993	SRP213938	PRJNA553572	A map of cis regulatory elements and 3D genome structures in zebrafish	GSE134055	Other	The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.		pubmed:33239788;pubmed:35649578		YueLab RNA seq Blood rep1	GSM4662085		source name:YueLab RNA seq Blood\|strain:Tuebingen\|tissue:Blood	YueLab RNA seq Blood rep1	RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac H3K4me3 ChIP seq were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain we called the peak using Homer with the parameter “ region size 1000” and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged	YueLab RNA seq Blood		RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext…	RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq ATAC seq Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions	strain:Tuebingen\|tissue:Blood	GSM4662085	GSM4662085: YueLab RNA seq Blood rep1; Danio rerio; RNA Seq	GSM4662085		1	RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext…	GEO Accession:GSM4662085	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP213938			YueLab-RNA-seq-Blood-rep1_1.fastq.gz YueLab-RNA-seq-Blood-rep1_2.fastq.gz	fastq fastq	10181340496.0	33713048.0	GSM4662085 r1	0:151 1:151	A:2735674306;C:2352790027;G:2376786768;T:2715986044;N:103351	151	151			2735674306	2352790027	2376786768	2715986044	103351	SRX8688332	SRS6966993	SRA919194	GEO	Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine	2	0.91563	0.91373	0.11339	0.11315	0.82235	0.82266	0.48854	0.48669	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	sc	single_cell_droplet	10x	United States	2020-07-08	Pharyngula	Embryo	Blood	Hematopoietic System
53493	53493	SRR9881612	SRX6634133	SRS5205093	SRP217216	PRJNA558070	N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells	GSE135246	Transcriptome Analysis	Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds		pubmed:33273096		223mut 27hpf EC1	GSM3996907		source name:endothelial cell\|tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303\|genotype:223mut	223mut 27hpf EC1	The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition.	endothelial cell		Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1	Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.	tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303\|genotype:223mut	GSM3996907	GSM3996907: 223mut 27hpf EC1; Danio rerio; RNA Seq	GSM3996907		1	Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1	GEO Accession:GSM3996907	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217216			Mut_pssorted_genome_bam.bam	10X Genomics bam file	31174899854.0	318111223.0	GSM3996907 r1	0:98	A:8464403532;C:7291172763;G:7282393533;T:8131647604;N:5282422	98				8464403532	7291172763	7282393533	8131647604	5282422	SRX6634133	SRS5205093	SRA930499	GEO	Internal Medicine, Yale University	1	0.92745		0.05306		0.84502		0.46383		98		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	sc	single_cell_droplet	10x	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
53494	53494	SRR9881611	SRX6634132	SRS5205092	SRP217216	PRJNA558070	N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells	GSE135246	Transcriptome Analysis	Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds		pubmed:33273096		wildtype 27hpf EC1	GSM3996906		source name:endothelial cell\|tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896\|genotype:wildtype	wildtype 27hpf EC1	The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition.	endothelial cell		Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1	Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.	tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896\|genotype:wildtype	GSM3996906	GSM3996906: wildtype 27hpf EC1; Danio rerio; RNA Seq	GSM3996906		1	Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1	GEO Accession:GSM3996906	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217216			WT_pssorted_genome_bam.bam	10X Genomics bam file	26866951370.0	274152565.0	GSM3996906 r1	0:98	A:7373453026;C:6169004304;G:6196779570;T:7121490110;N:6224360	98				7373453026	6169004304	6196779570	7121490110	6224360	SRX6634132	SRS5205092	SRA930499	GEO	Internal Medicine, Yale University	1	0.93015		0.0602		0.83853		0.4683		98		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	sc	single_cell_droplet	10x	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
54192	54192	SRR10095968	SRX6828141	SRS5370316	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					1b		strain:Tgolig2:GFPvu12\|age:1 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:1b\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	1b	1b	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP221273		loader:latf load	olig2gfp24hb_S2_L001_R1_001.fastq olig2gfp24hb_S2_L001_R2_001.fastq olig2gfp24hb_S2_L002_R1_001.fastq olig2gfp24hb_S2_L002_R2_001.fastq olig2gfp24hb_S2_L003_R1_001.fastq olig2gfp24hb_S2_L003_R2_001.fastq olig2gfp24hb_S2_L004_R1_001.fastq olig2gfp24hb_S2_L004_R2_001.fastq olig2gfp24hb_S2_L005_R1_001.fastq olig2gfp24hb_S2_L005_R2_001.fastq olig2gfp24hb_S2_L006_R1_001.fastq olig2gfp24hb_S2_L006_R2_001.fastq olig2gfp24hb_S2_L007_R1_001.fastq olig2gfp24hb_S2_L007_R2_001.fastq olig2gfp24hb_S2_L008_R1_001.fastq olig2gfp24hb_S2_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	98193351273.0	617568247.0	1b.gz	0:26 1:133	A:27237053473;C:21828277485;G:22951157364;T:26162156154;N:14706797	26	133			27237053473	21828277485	22951157364	26162156154	14706797	SRX6828141	SRS5370316	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.01479	0.95138	0.00273	0.12104	0.97327	0.78293	0.39405	0.4998	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
54193	54193	SRR10095969	SRX6828140	SRS5370315	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					1a		strain:Tgolig2:GFPvu12\|age:1 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:1a\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	1a	1a	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP221273		loader:latf load	olig2gfp24ha_S1_L001_R1_001.fastq olig2gfp24ha_S1_L001_R2_001.fastq olig2gfp24ha_S1_L002_R1_001.fastq olig2gfp24ha_S1_L002_R2_001.fastq olig2gfp24ha_S1_L003_R1_001.fastq olig2gfp24ha_S1_L003_R2_001.fastq olig2gfp24ha_S1_L004_R1_001.fastq olig2gfp24ha_S1_L004_R2_001.fastq olig2gfp24ha_S1_L005_R1_001.fastq olig2gfp24ha_S1_L005_R2_001.fastq olig2gfp24ha_S1_L006_R1_001.fastq olig2gfp24ha_S1_L006_R2_001.fastq olig2gfp24ha_S1_L007_R1_001.fastq olig2gfp24ha_S1_L007_R2_001.fastq olig2gfp24ha_S1_L008_R1_001.fastq olig2gfp24ha_S1_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	99552249225.0	626114775.0	1a.gz	0:26 1:133	A:27540748865;C:22111148705;G:23108024457;T:26777444676;N:14882522	26	133			27540748865	22111148705	23108024457	26777444676	14882522	SRX6828140	SRS5370315	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.01166	0.95413	0.002	0.08635	0.9779	0.80034	0.44044	0.48046	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
55640	55640	SRR10586526	SRX7266919	SRS5761461	SRP234691	PRJNA593445	A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq]	GSE141427	Transcriptome Analysis	Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000.	parent bioproject:PRJNA593433	pubmed:32094115		44hpf Hindbrain scRNA seq	GSM4202682		source name:Dissected hindbrain and surrounding tissues\|tissue:Dissected hindbrain and surrounding tissues\|Stage:44hpf\|strain:LondonAB\|genotype:wt\|growth:25°C	44hpf Hindbrain scRNA seq	10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts	Dissected hindbrain and surrounding tissues		Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles		tissue:Dissected hindbrain and surrounding tissues\|Stage:44hpf\|strain:LondonAB\|genotype:wt\|growth:25°C	GSM4202682	GSM4202682: 44hpf Hindbrain scRNA seq; Danio rerio; RNA Seq	GSM4202682		1	Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles	GEO Accession:GSM4202682	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP234691		loader:fastq load.py\|options: readTypes=TTB read1PairFiles=MT 10X240118 S1 L006 I1 001.fastq.gz read2PairFiles=MT 10X240118 S1 L006 R1 001.fastq.gz read3PairFiles=MT 10X240118 S1 L006 R2 001.fastq.gz	MT_10X240118_S1_L006_R2_001.fastq.gz MT_10X240118_S1_L006_R1_001.fastq.gz MT_10X240118_S1_L006_I1_001.fastq.gz	fastq fastq fastq	67359962250.0	320761725.0	GSM4202682 r1	0:8 1:101 2:101	A:16212646159;C:11777426351;G:12335518595;T:27032040933;N:2330212	8	101	101		16212646159	11777426351	12335518595	27032040933	2330212	SRX7266919	SRS5761461	SRA1006557	GEO	The Francis Crick Institute	1	0.9195		0.12389		0.82593		0.50909		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2019-12-04	Pharyngula	Embryo	Brain	Nervous System
55641	55641	SRR10586525	SRX7266917	SRS5761460	SRP234691	PRJNA593445	A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq]	GSE141427	Transcriptome Analysis	Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000.	parent bioproject:PRJNA593433	pubmed:32094115		24hpf Hindbrain scRNA seq	GSM4202681		source name:Dissected hindbrain and surrounding tissues\|tissue:Dissected hindbrain and surrounding tissues\|Stage:24hpf\|strain:LondonAB\|genotype:wt\|growth:28.5°C	24hpf Hindbrain scRNA seq	10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts	Dissected hindbrain and surrounding tissues		Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles		tissue:Dissected hindbrain and surrounding tissues\|Stage:24hpf\|strain:LondonAB\|genotype:wt\|growth:28.5°C	GSM4202681	GSM4202681: 24hpf Hindbrain scRNA seq; Danio rerio; RNA Seq	GSM4202681		1	Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles	GEO Accession:GSM4202681	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP234691		loader:fastq load.py\|options: readTypes=TTB read1PairFiles=TAM677A2 S7 L008 I1 001.fastq.gz read2PairFiles=TAM677A2 S7 L008 R1 001.fastq.gz read3PairFiles=TAM677A2 S7 L008 R2 001.fastq.gz	TAM677A2_S7_L008_I1_001.fastq.gz TAM677A2_S7_L008_R1_001.fastq.gz TAM677A2_S7_L008_R2_001.fastq.gz	fastq fastq fastq	71824244730.0	342020213.0	GSM4202681 r1	0:8 1:101 2:101	A:16595981302;C:11865598791;G:12955979417;T:30401981747;N:4703473	8	101	101		16595981302	11865598791	12955979417	30401981747	4703473	SRX7266917	SRS5761460	SRA1006557	GEO	The Francis Crick Institute	1	0.92906		0.11719		0.80982		0.52506		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2019-12-04	Pharyngula	Embryo	Brain	Nervous System
55649	55649	SRR10611686	SRX7290958	SRS5784121	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.				BP 30h	GSM4210785		source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:30hpf\|exposed pollutants:100ppb BPA	BP 30h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:30hpf\|exposed pollutants:100ppb BPA	GSM4210785	GSM4210785: BP 30h; Danio rerio; RNA Seq	GSM4210785		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210785	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262			BP-30h_S6_L006_R1_001.fastq.gz BP-30h_S6_L006_R2_001.fastq.gz	fastq fastq	123297367860.0	408269430.0	GSM4210785 r1	0:151 1:151	A:29612865612;C:21327621660;G:21810738134;T:50523353893;N:22788561	151	151			29612865612	21327621660	21810738134	50523353893	22788561	SRX7290958	SRS5784121	SRA1008496	GEO	Nanjing University	2	0.07493	0.92162	0.00891	0.06219	0.98299	0.81594	0.48492	0.48154	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
55652	55652	SRR10611683	SRX7290955	SRS5784116	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.				CK 30h	GSM4210782		source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:30hpf\|exposed pollutants:n1	CK 30h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:30hpf\|exposed pollutants:n1	GSM4210782	GSM4210782: CK 30h; Danio rerio; RNA Seq	GSM4210782		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210782	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262			CK-30h_S5_L005_R1_001.fastq.gz CK-30h_S5_L005_R2_001.fastq.gz	fastq fastq	106224273812.0	351736006.0	GSM4210782 r1	0:151 1:151	A:25405444654;C:18089775514;G:18594095209;T:44115027002;N:19931433	151	151			25405444654	18089775514	18594095209	44115027002	19931433	SRX7290955	SRS5784116	SRA1008496	GEO	Nanjing University	2	0.06113	0.92264	0.00743	0.0605	0.98415	0.81675	0.50316	0.47382	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
59292	59292	SRR11811475	SRX8362742	SRS6678633	SRP262311	PRJNA633835	Single cell RNA seq and ATAC seq of zebrafish retina	GSE150839	Other	To study the transcriptomic and chromatin accessibility heterogeneity of zebrafish retinal progenitor cells Overall design: 2 retinal samples from embryonic zebrafish		pubmed:32699896		RNA seq retina atoh7 44hpf	GSM4559534		source name:retina\|strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP\|tissue:retina\|developmental stage:44 hpf	RNA seq retina atoh7 44hpf	Raw datasets of single cell RNA seq were aligned zebrafish genome GRCz10 filtered and counted using the Cell Ranger software v2.1.0 10x Genomics to generate the processed matrix data. Raw data of single cell ATAC seq were aligned zebrafish genome GRCz10 filtered and counted using the Cell Ranger ATAC software v1.1 10x Genomics to generated the processed matrix data. Genome build: GRCz10 Supplementary files format and content: Processed data files are in tar.gz format containing matrix files for further analysis.	retina		Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single cell RNA seq. The single nuclei were further extracted by digitonin for single cell ATAC seq. The libraries were constructed using the Chromium Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x genomics PN 120237 or the Chromium Single Cell ATAC Library & Gel Bead Kit 10x genomics following the manufacturer’s protocol		strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP\|tissue:retina\|developmental stage:44 hpf	GSM4559534	GSM4559534: RNA seq retina atoh7 44hpf; Danio rerio; RNA Seq	GSM4559534		1	Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single cell RNA seq. The single nuclei were further extracted by digitonin for single cell ATAC seq. The libraries were constructed using the Chromium Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x genomics PN 120237 or the Chromium Single Cell ATAC Library & Gel Bead Kit 10x genomics following the manufacturer's protocol	GEO Accession:GSM4559534	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP262311		intentional duplicate\|options: max err count 100000000	atoh7_scRNA_bam.bam	10X Genomics bam file	61111212107.0	414028035.0	GSM4559534 r1	0:147.60	A:18052310869;C:12727112571;G:14225357068;T:16105981406;N:450193	147				18052310869	12727112571	14225357068	16105981406	450193	SRX8362742	SRS6678633	SRA1077074	GEO	Institute of Neuroscience, Chinese Academy of Sciences	1	0.89647		0.06712		0.85228		0.50102		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-05-19	Pharyngula	Embryo	Eye	Sensory System
59887	59887	SRR12067711	SRX8595501	SRS6886082	SRP268312	PRJNA641114	Single cell transcriptomic analysis 30 hpf Zebrafish trunks	GSE152982	Other	Here we performed single cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified spanning all three embryonic germ layers. Overall design: Whole trunks excised from 30 embryos at 30 hpf were dissociated using a cold protease dissociation protocol. Barcoding of cells and and cDNA library construction was carried out using 10X Genomics' Chromium platform.		pubmed:34234366		Zf 30h trunk	GSM4631066		source name:Zebrafish Trunks\|age:30 hpf\|tissue:trunk\|genotype:wildtype	Zf 30h trunk	All processing was performed in 10X Genomics CellRanger v3.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.11 and to obtain the gene expression matrices Genome build: GRCz11 Supplementary files format and content: mtx matrix files	Zebrafish Trunks		Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol		age:30 hpf\|tissue:trunk\|genotype:wildtype	GSM4631066	GSM4631066: Zf 30h trunk; Danio rerio; RNA Seq	GSM4631066		1	Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol	GEO Accession:GSM4631066	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP268312		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Zf30hTrunk S1 L001 I1 001.fastq.gz read2PairFiles=Zf30hTrunk S1 L001 R1 001.fastq.gz read3PairFiles=Zf30hTrunk S1 L001 R2 001.fastq.gz	Zf30hTrunk_S1_L001_I1_001.fastq.gz Zf30hTrunk_S1_L001_R1_001.fastq.gz Zf30hTrunk_S1_L001_R2_001.fastq.gz	fastq fastq fastq	30568523622.0	167958921.0	GSM4631066 r1	0:8 1:27 2:147	A:8739694698;C:6736998816;G:6903125001;T:8168427703;N:20277404	8	27	147		8739694698	6736998816	6903125001	8168427703	20277404	SRX8595501	SRS6886082	SRA1089692	GEO	University of South Florida	1	0.88066		0.09296		0.8506		0.50586		147		B		usable mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	nextera	sc	single_cell_droplet	10x	United States	2020-06-22	Pharyngula	Embryo	Trunk	Surface Structure
59888	59888	SRR12067712	SRX8595501	SRS6886082	SRP268312	PRJNA641114	Single cell transcriptomic analysis 30 hpf Zebrafish trunks	GSE152982	Other	Here we performed single cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified spanning all three embryonic germ layers. Overall design: Whole trunks excised from 30 embryos at 30 hpf were dissociated using a cold protease dissociation protocol. Barcoding of cells and and cDNA library construction was carried out using 10X Genomics' Chromium platform.		pubmed:34234366		Zf 30h trunk	GSM4631066		source name:Zebrafish Trunks\|age:30 hpf\|tissue:trunk\|genotype:wildtype	Zf 30h trunk	All processing was performed in 10X Genomics CellRanger v3.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.11 and to obtain the gene expression matrices Genome build: GRCz11 Supplementary files format and content: mtx matrix files	Zebrafish Trunks		Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol		age:30 hpf\|tissue:trunk\|genotype:wildtype	GSM4631066	GSM4631066: Zf 30h trunk; Danio rerio; RNA Seq	GSM4631066		1	Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single cell suspensions were processed through the Chromium platform 10X Genomics to generate single cell cDNA libraries cDNA was amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol	GEO Accession:GSM4631066	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP268312		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Zf30hTrunk S1 L002 I1 001.fastq.gz read2PairFiles=Zf30hTrunk S1 L002 R1 001.fastq.gz read3PairFiles=Zf30hTrunk S1 L002 R2 001.fastq.gz	Zf30hTrunk_S1_L002_I1_001.fastq.gz Zf30hTrunk_S1_L002_R1_001.fastq.gz Zf30hTrunk_S1_L002_R2_001.fastq.gz	fastq fastq fastq	31428372976.0	172683368.0	GSM4631066 r2	0:8 1:27 2:147	A:8978925123;C:6926043302;G:7091713953;T:8399543364;N:32147234	8	27	147		8978925123	6926043302	7091713953	8399543364	32147234	SRX8595501	SRS6886082	SRA1089692	GEO	University of South Florida	1	0.87666		0.09235		0.85277		0.49776		147		B		usable mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	nextera	sc	single_cell_droplet	10x	United States	2020-06-22	Pharyngula	Embryo	Trunk	Surface Structure
60591	60591	SRR12424274	SRX8920144	SRS7176692	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 36hpf	GSM4718657		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718657	GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq	GSM4718657		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_36hfp_1_S69_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_1_S69_L001_R2_001.fastq.gz	fastq fastq	13366864582.0	44261141.0	GSM4718657 r1	0:151 1:151	A:3721647646;C:2385939960;G:3494552257;T:3764514262;N:210457	151	151			3721647646	2385939960	3494552257	3764514262	210457	SRX8920144	SRS7176692	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.85449	0.0	0.08264	1.0	0.84086		0.50156	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60592	60592	SRR12424275	SRX8920144	SRS7176692	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 36hpf	GSM4718657		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718657	GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq	GSM4718657		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_36hfp_2_S70_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_2_S70_L001_R2_001.fastq.gz	fastq fastq	10606211914.0	35119907.0	GSM4718657 r2	0:151 1:151	A:2974656607;C:1869869441;G:2750621038;T:3010898673;N:166155	151	151			2974656607	1869869441	2750621038	3010898673	166155	SRX8920144	SRS7176692	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.84822	0.0	0.08456	1.0	0.83719		0.51503	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60593	60593	SRR12424276	SRX8920144	SRS7176692	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 36hpf	GSM4718657		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718657	GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq	GSM4718657		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_36hfp_3_S71_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_3_S71_L001_R2_001.fastq.gz	fastq fastq	15614508642.0	51703671.0	GSM4718657 r3	0:151 1:151	A:4330312984;C:2826855730;G:4093245712;T:4363847925;N:246291	151	151			4330312984	2826855730	4093245712	4363847925	246291	SRX8920144	SRS7176692	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.8543	0.0	0.08219	1.0	0.83727		0.51892	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60594	60594	SRR12424277	SRX8920144	SRS7176692	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 36hpf	GSM4718657		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718657	GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq	GSM4718657		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_36hfp_4_S72_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_4_S72_L001_R2_001.fastq.gz	fastq fastq	10707787198.0	35456249.0	GSM4718657 r4	0:151 1:151	A:2981466900;C:1909696186;G:2797297473;T:3019156550;N:170089	151	151			2981466900	1909696186	2797297473	3019156550	170089	SRX8920144	SRS7176692	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.85466	0.0	0.08381	1.0	0.83562		0.51035	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60595	60595	SRR12424270	SRX8920143	SRS7176691	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 24hpf	GSM4718656		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718656	GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq	GSM4718656		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_24hfp_1_S10_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_1_S10_L001_R2_001.fastq.gz	fastq fastq	21279021170.0	70460335.0	GSM4718656 r1	0:151 1:151	A:5842145219;C:3712477572;G:5933108587;T:5790922441;N:367351	151	151			5842145219	3712477572	5933108587	5790922441	367351	SRX8920143	SRS7176691	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.83071	0.0	0.06828	1.0	0.8406		0.5078	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60596	60596	SRR12424271	SRX8920143	SRS7176691	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 24hpf	GSM4718656		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718656	GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq	GSM4718656		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_24hfp_2_S20_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_2_S20_L001_R2_001.fastq.gz	fastq fastq	22414094210.0	74218855.0	GSM4718656 r2	0:151 1:151	A:6145677154;C:3904876630;G:6254105391;T:6109049174;N:385861	151	151			6145677154	3904876630	6254105391	6109049174	385861	SRX8920143	SRS7176691	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.83148	0.0	0.06914	1.0	0.84033		0.49666	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60597	60597	SRR12424272	SRX8920143	SRS7176691	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 24hpf	GSM4718656		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718656	GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq	GSM4718656		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_24hfp_3_S30_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_3_S30_L001_R2_001.fastq.gz	fastq fastq	16406166006.0	54325053.0	GSM4718656 r3	0:151 1:151	A:4513103872;C:2865727260;G:4569430659;T:4457621166;N:283049	151	151			4513103872	2865727260	4569430659	4457621166	283049	SRX8920143	SRS7176691	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.82928	0.0	0.06878	1.0	0.83989		0.4916	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60598	60598	SRR12424273	SRX8920143	SRS7176691	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 24hpf	GSM4718656		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718656	GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq	GSM4718656		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_24hfp_4_S40_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_4_S40_L001_R2_001.fastq.gz	fastq fastq	17382967792.0	57559496.0	GSM4718656 r4	0:151 1:151	A:4767137063;C:3044788720;G:4846983492;T:4723757048;N:301469	151	151			4767137063	3044788720	4846983492	4723757048	301469	SRX8920143	SRS7176691	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.83084	0.0	0.06779	1.0	0.83948		0.49689	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
61265	61265	SRR12661716	SRX9142583	SRS7383887	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf2 S7	GSM4793200		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf2 S7	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793200	GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq	GSM4793200		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793200	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2 S7 L001 I1 001.fastq.gz read2PairFiles=zBr36hpf2 S7 L001 R1 001.fastq.gz read3PairFiles=zBr36hpf2 S7 L001 R2 001.fastq.gz	zBr36hpf2_S7_L001_I1_001.fastq.gz zBr36hpf2_S7_L001_R1_001.fastq.gz zBr36hpf2_S7_L001_R2_001.fastq.gz	fastq fastq fastq	1354796416.0	14726048.0	GSM4793200 r1	0:8 1:26 2:58	A:361641217;C:295707879;G:331919755;T:363556787;N:1970778	8	26	58		361641217	295707879	331919755	363556787	1970778	SRX9142583	SRS7383887	SRA1127180	GEO	Harvard University	1	0.94293		0.09579		0.80659		0.48535		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61266	61266	SRR12661717	SRX9142583	SRS7383887	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf2 S7	GSM4793200		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf2 S7	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793200	GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq	GSM4793200		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793200	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2 S7 L002 I1 001.fastq.gz read2PairFiles=zBr36hpf2 S7 L002 R1 001.fastq.gz read3PairFiles=zBr36hpf2 S7 L002 R2 001.fastq.gz	zBr36hpf2_S7_L002_I1_001.fastq.gz zBr36hpf2_S7_L002_R1_001.fastq.gz zBr36hpf2_S7_L002_R2_001.fastq.gz	fastq fastq fastq	1358239516.0	14763473.0	GSM4793200 r2	0:8 1:26 2:58	A:361906449;C:296366138;G:333591075;T:364374247;N:2001607	8	26	58		361906449	296366138	333591075	364374247	2001607	SRX9142583	SRS7383887	SRA1127180	GEO	Harvard University	1	0.94081		0.09328		0.80497		0.48086		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61267	61267	SRR12661718	SRX9142583	SRS7383887	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf2 S7	GSM4793200		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf2 S7	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793200	GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq	GSM4793200		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793200	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2 S7 L003 I1 001.fastq.gz read2PairFiles=zBr36hpf2 S7 L003 R1 001.fastq.gz read3PairFiles=zBr36hpf2 S7 L003 R2 001.fastq.gz	zBr36hpf2_S7_L003_I1_001.fastq.gz zBr36hpf2_S7_L003_R1_001.fastq.gz zBr36hpf2_S7_L003_R2_001.fastq.gz	fastq fastq fastq	1370706988.0	14898989.0	GSM4793200 r3	0:8 1:26 2:58	A:364455570;C:298700749;G:338352913;T:367620807;N:1576949	8	26	58		364455570	298700749	338352913	367620807	1576949	SRX9142583	SRS7383887	SRA1127180	GEO	Harvard University	1	0.94035		0.09554		0.80474		0.48964		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61268	61268	SRR12661719	SRX9142583	SRS7383887	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf2 S7	GSM4793200		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf2 S7	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793200	GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq	GSM4793200		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793200	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2 S7 L004 I1 001.fastq.gz read2PairFiles=zBr36hpf2 S7 L004 R1 001.fastq.gz read3PairFiles=zBr36hpf2 S7 L004 R2 001.fastq.gz	zBr36hpf2_S7_L004_I1_001.fastq.gz zBr36hpf2_S7_L004_R1_001.fastq.gz zBr36hpf2_S7_L004_R2_001.fastq.gz	fastq fastq fastq	1366604800.0	14854400.0	GSM4793200 r4	0:8 1:26 2:58	A:364547650;C:298236417;G:335364562;T:366845359;N:1610812	8	26	58		364547650	298236417	335364562	366845359	1610812	SRX9142583	SRS7383887	SRA1127180	GEO	Harvard University	1	0.94169		0.09572		0.8076		0.49419		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61269	61269	SRR12661720	SRX9142583	SRS7383887	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf2 S7	GSM4793200		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf2 S7	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793200	GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq	GSM4793200		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793200	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2b S7 L001 I1 001.fastq.gz read2PairFiles=zBr36hpf2b S7 L001 R1 001.fastq.gz read3PairFiles=zBr36hpf2b S7 L001 R2 001.fastq.gz	zBr36hpf2b_S7_L001_I1_001.fastq.gz zBr36hpf2b_S7_L001_R1_001.fastq.gz zBr36hpf2b_S7_L001_R2_001.fastq.gz	fastq fastq fastq	1405330268.0	15275329.0	GSM4793200 r5	0:8 1:26 2:58	A:375342661;C:306451867;G:346478190;T:376672948;N:384602	8	26	58		375342661	306451867	346478190	376672948	384602	SRX9142583	SRS7383887	SRA1127180	GEO	Harvard University	1	0.94163		0.09494		0.80813		0.4829		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61270	61270	SRR12661721	SRX9142583	SRS7383887	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf2 S7	GSM4793200		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf2 S7	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793200	GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq	GSM4793200		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793200	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2b S7 L002 I1 001.fastq.gz read2PairFiles=zBr36hpf2b S7 L002 R1 001.fastq.gz read3PairFiles=zBr36hpf2b S7 L002 R2 001.fastq.gz	zBr36hpf2b_S7_L002_I1_001.fastq.gz zBr36hpf2b_S7_L002_R1_001.fastq.gz zBr36hpf2b_S7_L002_R2_001.fastq.gz	fastq fastq fastq	1394928748.0	15162269.0	GSM4793200 r6	0:8 1:26 2:58	A:372974203;C:304436911;G:343375665;T:373791458;N:350511	8	26	58		372974203	304436911	343375665	373791458	350511	SRX9142583	SRS7383887	SRA1127180	GEO	Harvard University	1	0.9424		0.0951		0.80689		0.48817		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61271	61271	SRR12661722	SRX9142583	SRS7383887	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf2 S7	GSM4793200		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf2 S7	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793200	GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq	GSM4793200		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793200	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2b S7 L003 I1 001.fastq.gz read2PairFiles=zBr36hpf2b S7 L003 R1 001.fastq.gz read3PairFiles=zBr36hpf2b S7 L003 R2 001.fastq.gz	zBr36hpf2b_S7_L003_I1_001.fastq.gz zBr36hpf2b_S7_L003_R1_001.fastq.gz zBr36hpf2b_S7_L003_R2_001.fastq.gz	fastq fastq fastq	1395591792.0	15169476.0	GSM4793200 r7	0:8 1:26 2:58	A:372521506;C:304137483;G:344538336;T:374208291;N:186176	8	26	58		372521506	304137483	344538336	374208291	186176	SRX9142583	SRS7383887	SRA1127180	GEO	Harvard University	1	0.94224		0.09336		0.80886		0.48266		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61272	61272	SRR12661723	SRX9142583	SRS7383887	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf2 S7	GSM4793200		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf2 S7	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793200	GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq	GSM4793200		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793200	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2b S7 L004 I1 001.fastq.gz read2PairFiles=zBr36hpf2b S7 L004 R1 001.fastq.gz read3PairFiles=zBr36hpf2b S7 L004 R2 001.fastq.gz	zBr36hpf2b_S7_L004_I1_001.fastq.gz zBr36hpf2b_S7_L004_R1_001.fastq.gz zBr36hpf2b_S7_L004_R2_001.fastq.gz	fastq fastq fastq	1284456068.0	13961479.0	GSM4793200 r8	0:8 1:26 2:58	A:345006052;C:280180152;G:313982801;T:345126707;N:160356	8	26	58		345006052	280180152	313982801	345126707	160356	SRX9142583	SRS7383887	SRA1127180	GEO	Harvard University	1	0.9426		0.09636		0.81373		0.48776		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61273	61273	SRR12661708	SRX9142582	SRS7383886	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf1 S8	GSM4793199		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf1 S8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793199	GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq	GSM4793199		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1 S8 L001 I1 001.fastq.gz read2PairFiles=zBr36hpf1 S8 L001 R1 001.fastq.gz read3PairFiles=zBr36hpf1 S8 L001 R2 001.fastq.gz	zBr36hpf1_S8_L001_I1_001.fastq.gz zBr36hpf1_S8_L001_R1_001.fastq.gz zBr36hpf1_S8_L001_R2_001.fastq.gz	fastq fastq fastq	1311331568.0	14253604.0	GSM4793199 r1	0:8 1:26 2:58	A:349311358;C:289871823;G:320764029;T:349490594;N:1893764	8	26	58		349311358	289871823	320764029	349490594	1893764	SRX9142582	SRS7383886	SRA1127180	GEO	Harvard University	1	0.94285		0.09707		0.80543		0.50628		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61274	61274	SRR12661709	SRX9142582	SRS7383886	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf1 S8	GSM4793199		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf1 S8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793199	GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq	GSM4793199		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1 S8 L002 I1 001.fastq.gz read2PairFiles=zBr36hpf1 S8 L002 R1 001.fastq.gz read3PairFiles=zBr36hpf1 S8 L002 R2 001.fastq.gz	zBr36hpf1_S8_L002_I1_001.fastq.gz zBr36hpf1_S8_L002_R1_001.fastq.gz zBr36hpf1_S8_L002_R2_001.fastq.gz	fastq fastq fastq	1314508604.0	14288137.0	GSM4793199 r2	0:8 1:26 2:58	A:349593185;C:290464605;G:322339344;T:350190708;N:1920762	8	26	58		349593185	290464605	322339344	350190708	1920762	SRX9142582	SRS7383886	SRA1127180	GEO	Harvard University	1	0.94186		0.09781		0.806		0.49005		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61275	61275	SRR12661710	SRX9142582	SRS7383886	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf1 S8	GSM4793199		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf1 S8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793199	GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq	GSM4793199		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1 S8 L003 I1 001.fastq.gz read2PairFiles=zBr36hpf1 S8 L003 R1 001.fastq.gz read3PairFiles=zBr36hpf1 S8 L003 R2 001.fastq.gz	zBr36hpf1_S8_L003_I1_001.fastq.gz zBr36hpf1_S8_L003_R1_001.fastq.gz zBr36hpf1_S8_L003_R2_001.fastq.gz	fastq fastq fastq	1323431500.0	14385125.0	GSM4793199 r3	0:8 1:26 2:58	A:351235327;C:292146627;G:326032256;T:352503850;N:1513440	8	26	58		351235327	292146627	326032256	352503850	1513440	SRX9142582	SRS7383886	SRA1127180	GEO	Harvard University	1	0.94259		0.09668		0.80456		0.4837		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61276	61276	SRR12661711	SRX9142582	SRS7383886	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf1 S8	GSM4793199		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf1 S8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793199	GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq	GSM4793199		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1 S8 L004 I1 001.fastq.gz read2PairFiles=zBr36hpf1 S8 L004 R1 001.fastq.gz read3PairFiles=zBr36hpf1 S8 L004 R2 001.fastq.gz	zBr36hpf1_S8_L004_I1_001.fastq.gz zBr36hpf1_S8_L004_R1_001.fastq.gz zBr36hpf1_S8_L004_R2_001.fastq.gz	fastq fastq fastq	1323552940.0	14386445.0	GSM4793199 r4	0:8 1:26 2:58	A:352361534;C:292521995;G:324227981;T:352876234;N:1565196	8	26	58		352361534	292521995	324227981	352876234	1565196	SRX9142582	SRS7383886	SRA1127180	GEO	Harvard University	1	0.94286		0.09605		0.80436		0.49703		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61277	61277	SRR12661712	SRX9142582	SRS7383886	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf1 S8	GSM4793199		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf1 S8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793199	GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq	GSM4793199		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1b S8 L001 I1 001.fastq.gz read2PairFiles=zBr36hpf1b S8 L001 R1 001.fastq.gz read3PairFiles=zBr36hpf1b S8 L001 R2 001.fastq.gz	zBr36hpf1b_S8_L001_I1_001.fastq.gz zBr36hpf1b_S8_L001_R1_001.fastq.gz zBr36hpf1b_S8_L001_R2_001.fastq.gz	fastq fastq fastq	1352165032.0	14697446.0	GSM4793199 r5	0:8 1:26 2:58	A:360326597;C:298694884;G:332801734;T:359971929;N:369888	8	26	58		360326597	298694884	332801734	359971929	369888	SRX9142582	SRS7383886	SRA1127180	GEO	Harvard University	1	0.94237		0.09683		0.80768		0.48464		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61278	61278	SRR12661713	SRX9142582	SRS7383886	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf1 S8	GSM4793199		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf1 S8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793199	GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq	GSM4793199		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1b S8 L002 I1 001.fastq.gz read2PairFiles=zBr36hpf1b S8 L002 R1 001.fastq.gz read3PairFiles=zBr36hpf1b S8 L002 R2 001.fastq.gz	zBr36hpf1b_S8_L002_I1_001.fastq.gz zBr36hpf1b_S8_L002_R1_001.fastq.gz zBr36hpf1b_S8_L002_R2_001.fastq.gz	fastq fastq fastq	1344669976.0	14615978.0	GSM4793199 r6	0:8 1:26 2:58	A:358739497;C:297264368;G:330471655;T:357861866;N:332590	8	26	58		358739497	297264368	330471655	357861866	332590	SRX9142582	SRS7383886	SRA1127180	GEO	Harvard University	1	0.94299		0.09714		0.80793		0.49394		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61279	61279	SRR12661714	SRX9142582	SRS7383886	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf1 S8	GSM4793199		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf1 S8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793199	GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq	GSM4793199		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1b S8 L003 I1 001.fastq.gz read2PairFiles=zBr36hpf1b S8 L003 R1 001.fastq.gz read3PairFiles=zBr36hpf1b S8 L003 R2 001.fastq.gz	zBr36hpf1b_S8_L003_I1_001.fastq.gz zBr36hpf1b_S8_L003_R1_001.fastq.gz zBr36hpf1b_S8_L003_R2_001.fastq.gz	fastq fastq fastq	1340447268.0	14570079.0	GSM4793199 r7	0:8 1:26 2:58	A:356994310;C:295934792;G:330308810;T:357032061;N:177295	8	26	58		356994310	295934792	330308810	357032061	177295	SRX9142582	SRS7383886	SRA1127180	GEO	Harvard University	1	0.94211		0.0964		0.80868		0.49803		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61280	61280	SRR12661715	SRX9142582	SRS7383886	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr36hpf1 S8	GSM4793199		source name:zebrafish brain\|tissue:brain\|developmental stage:36hpf	zBr36hpf1 S8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:36hpf	GSM4793199	GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq	GSM4793199		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1b S8 L004 I1 001.fastq.gz read2PairFiles=zBr36hpf1b S8 L004 R1 001.fastq.gz read3PairFiles=zBr36hpf1b S8 L004 R2 001.fastq.gz	zBr36hpf1b_S8_L004_I1_001.fastq.gz zBr36hpf1b_S8_L004_R1_001.fastq.gz zBr36hpf1b_S8_L004_R2_001.fastq.gz	fastq fastq fastq	1233239116.0	13404773.0	GSM4793199 r8	0:8 1:26 2:58	A:330431166;C:272462685;G:301048391;T:329148018;N:148856	8	26	58		330431166	272462685	301048391	329148018	148856	SRX9142582	SRS7383886	SRA1127180	GEO	Harvard University	1	0.94278		0.09641		0.81012		0.49678		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61281	61281	SRR12661704	SRX9142581	SRS7383885	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf3 S2	GSM4793198		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf3 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793198	GSM4793198: zBr24hpf3 S2; Danio rerio; RNA Seq	GSM4793198		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf3 S2 L001 I1 001.fastq.gz read2PairFiles=zBr24hpf3 S2 L001 R1 001.fastq.gz read3PairFiles=zBr24hpf3 S2 L001 R2 001.fastq.gz	zBr24hpf3_S2_L001_I1_001.fastq.gz zBr24hpf3_S2_L001_R1_001.fastq.gz zBr24hpf3_S2_L001_R2_001.fastq.gz	fastq fastq fastq	1911367160.0	20775730.0	GSM4793198 r1	0:8 1:26 2:58	A:518555517;C:428251265;G:480738767;T:483105990;N:715621	8	26	58		518555517	428251265	480738767	483105990	715621	SRX9142581	SRS7383885	SRA1127180	GEO	Harvard University	1	0.94875		0.07782		0.83017		0.48957		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61282	61282	SRR12661705	SRX9142581	SRS7383885	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf3 S2	GSM4793198		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf3 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793198	GSM4793198: zBr24hpf3 S2; Danio rerio; RNA Seq	GSM4793198		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf3 S2 L002 I1 001.fastq.gz read2PairFiles=zBr24hpf3 S2 L002 R1 001.fastq.gz read3PairFiles=zBr24hpf3 S2 L002 R2 001.fastq.gz	zBr24hpf3_S2_L002_I1_001.fastq.gz zBr24hpf3_S2_L002_R1_001.fastq.gz zBr24hpf3_S2_L002_R2_001.fastq.gz	fastq fastq fastq	1768561540.0	19223495.0	GSM4793198 r2	0:8 1:26 2:58	A:492211957;C:396800414;G:429629025;T:449274681;N:645463	8	26	58		492211957	396800414	429629025	449274681	645463	SRX9142581	SRS7383885	SRA1127180	GEO	Harvard University	1	0.94574		0.08385		0.84964		0.47837		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61283	61283	SRR12661706	SRX9142581	SRS7383885	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf3 S2	GSM4793198		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf3 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793198	GSM4793198: zBr24hpf3 S2; Danio rerio; RNA Seq	GSM4793198		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf3 S2 L003 I1 001.fastq.gz read2PairFiles=zBr24hpf3 S2 L003 R1 001.fastq.gz read3PairFiles=zBr24hpf3 S2 L003 R2 001.fastq.gz	zBr24hpf3_S2_L003_I1_001.fastq.gz zBr24hpf3_S2_L003_R1_001.fastq.gz zBr24hpf3_S2_L003_R2_001.fastq.gz	fastq fastq fastq	1785914856.0	19412118.0	GSM4793198 r3	0:8 1:26 2:58	A:493608499;C:399868847;G:438420362;T:453669924;N:347224	8	26	58		493608499	399868847	438420362	453669924	347224	SRX9142581	SRS7383885	SRA1127180	GEO	Harvard University	1	0.94782		0.08226		0.84137		0.46993		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61284	61284	SRR12661707	SRX9142581	SRS7383885	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf3 S2	GSM4793198		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf3 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793198	GSM4793198: zBr24hpf3 S2; Danio rerio; RNA Seq	GSM4793198		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf3 S2 L004 I1 001.fastq.gz read2PairFiles=zBr24hpf3 S2 L004 R1 001.fastq.gz read3PairFiles=zBr24hpf3 S2 L004 R2 001.fastq.gz	zBr24hpf3_S2_L004_I1_001.fastq.gz zBr24hpf3_S2_L004_R1_001.fastq.gz zBr24hpf3_S2_L004_R2_001.fastq.gz	fastq fastq fastq	1783165344.0	19382232.0	GSM4793198 r4	0:8 1:26 2:58	A:495573405;C:399567193;G:434183228;T:453517782;N:323736	8	26	58		495573405	399567193	434183228	453517782	323736	SRX9142581	SRS7383885	SRA1127180	GEO	Harvard University	1	0.94802		0.08421		0.85131		0.4818		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61285	61285	SRR12661700	SRX9142580	SRS7383884	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf2 S4	GSM4793197		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf2 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793197	GSM4793197: zBr24hpf2 S4; Danio rerio; RNA Seq	GSM4793197		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793197	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf2 S4 L001 I1 001.fastq.gz read2PairFiles=zBr24hpf2 S4 L001 R1 001.fastq.gz read3PairFiles=zBr24hpf2 S4 L001 R2 001.fastq.gz	zBr24hpf2_S4_L001_I1_001.fastq.gz zBr24hpf2_S4_L001_R1_001.fastq.gz zBr24hpf2_S4_L001_R2_001.fastq.gz	fastq fastq fastq	1610567916.0	17506173.0	GSM4793197 r1	0:8 1:26 2:58	A:440549008;C:355249104;G:389445387;T:424941131;N:383286	8	26	58		440549008	355249104	389445387	424941131	383286	SRX9142580	SRS7383884	SRA1127180	GEO	Harvard University	1	0.93926		0.11249		0.82012		0.48613		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61286	61286	SRR12661701	SRX9142580	SRS7383884	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf2 S4	GSM4793197		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf2 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793197	GSM4793197: zBr24hpf2 S4; Danio rerio; RNA Seq	GSM4793197		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793197	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf2 S4 L002 I1 001.fastq.gz read2PairFiles=zBr24hpf2 S4 L002 R1 001.fastq.gz read3PairFiles=zBr24hpf2 S4 L002 R2 001.fastq.gz	zBr24hpf2_S4_L002_I1_001.fastq.gz zBr24hpf2_S4_L002_R1_001.fastq.gz zBr24hpf2_S4_L002_R2_001.fastq.gz	fastq fastq fastq	1584562552.0	17223506.0	GSM4793197 r2	0:8 1:26 2:58	A:436038687;C:349679779;G:380784321;T:417744447;N:315318	8	26	58		436038687	349679779	380784321	417744447	315318	SRX9142580	SRS7383884	SRA1127180	GEO	Harvard University	1	0.93966		0.1161		0.82217		0.47132		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61287	61287	SRR12661702	SRX9142580	SRS7383884	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf2 S4	GSM4793197		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf2 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793197	GSM4793197: zBr24hpf2 S4; Danio rerio; RNA Seq	GSM4793197		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793197	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf2 S4 L003 I1 001.fastq.gz read2PairFiles=zBr24hpf2 S4 L003 R1 001.fastq.gz read3PairFiles=zBr24hpf2 S4 L003 R2 001.fastq.gz	zBr24hpf2_S4_L003_I1_001.fastq.gz zBr24hpf2_S4_L003_R1_001.fastq.gz zBr24hpf2_S4_L003_R2_001.fastq.gz	fastq fastq fastq	1564085008.0	17000924.0	GSM4793197 r3	0:8 1:26 2:58	A:428352345;C:344229050;G:377948837;T:413305594;N:249182	8	26	58		428352345	344229050	377948837	413305594	249182	SRX9142580	SRS7383884	SRA1127180	GEO	Harvard University	1	0.93914		0.11487		0.82361		0.4832		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61288	61288	SRR12661703	SRX9142580	SRS7383884	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf2 S4	GSM4793197		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf2 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793197	GSM4793197: zBr24hpf2 S4; Danio rerio; RNA Seq	GSM4793197		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793197	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf2 S4 L004 I1 001.fastq.gz read2PairFiles=zBr24hpf2 S4 L004 R1 001.fastq.gz read3PairFiles=zBr24hpf2 S4 L004 R2 001.fastq.gz	zBr24hpf2_S4_L004_I1_001.fastq.gz zBr24hpf2_S4_L004_R1_001.fastq.gz zBr24hpf2_S4_L004_R2_001.fastq.gz	fastq fastq fastq	1618721692.0	17594801.0	GSM4793197 r4	0:8 1:26 2:58	A:441946732;C:356875026;G:392950304;T:426747266;N:202364	8	26	58		441946732	356875026	392950304	426747266	202364	SRX9142580	SRS7383884	SRA1127180	GEO	Harvard University	1	0.93904		0.11095		0.8196		0.47549		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61289	61289	SRR12661696	SRX9142579	SRS7383883	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf1 S3	GSM4793196		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf1 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793196	GSM4793196: zBr24hpf1 S3; Danio rerio; RNA Seq	GSM4793196		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793196	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf1 S3 L001 I1 001.fastq.gz read2PairFiles=zBr24hpf1 S3 L001 R1 001.fastq.gz read3PairFiles=zBr24hpf1 S3 L001 R2 001.fastq.gz	zBr24hpf1_S3_L001_I1_001.fastq.gz zBr24hpf1_S3_L001_R1_001.fastq.gz zBr24hpf1_S3_L001_R2_001.fastq.gz	fastq fastq fastq	1540025904.0	16739412.0	GSM4793196 r1	0:8 1:26 2:58	A:420531344;C:344603786;G:372689090;T:401831664;N:370020	8	26	58		420531344	344603786	372689090	401831664	370020	SRX9142579	SRS7383883	SRA1127180	GEO	Harvard University	1	0.93908		0.11195		0.82252		0.48589		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System
61290	61290	SRR12661697	SRX9142579	SRS7383883	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr24hpf1 S3	GSM4793196		source name:zebrafish brain\|tissue:brain\|developmental stage:24hpf	zBr24hpf1 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:24hpf	GSM4793196	GSM4793196: zBr24hpf1 S3; Danio rerio; RNA Seq	GSM4793196		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793196	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf1 S3 L002 I1 001.fastq.gz read2PairFiles=zBr24hpf1 S3 L002 R1 001.fastq.gz read3PairFiles=zBr24hpf1 S3 L002 R2 001.fastq.gz	zBr24hpf1_S3_L002_I1_001.fastq.gz zBr24hpf1_S3_L002_R1_001.fastq.gz zBr24hpf1_S3_L002_R2_001.fastq.gz	fastq fastq fastq	1516047116.0	16478773.0	GSM4793196 r2	0:8 1:26 2:58	A:416452609;C:339452130;G:364607393;T:395226361;N:308623	8	26	58		416452609	339452130	364607393	395226361	308623	SRX9142579	SRS7383883	SRA1127180	GEO	Harvard University	1	0.94016		0.11299		0.82315		0.49117		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Pharyngula	Embryo	Brain	Nervous System

Advanced export

JSON shape: default, array, newline-delimited

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");;