metadata: run_metadata: 466 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation

466 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
9898	9898	ERR4194114	ERX4155254	ERS4601292	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 2	SAMEA6873729	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873729\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 2\|age:8\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 2\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 2 s	Sample 2 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:8\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA8h_1_S2_L001.bam	bam	10087287534.0	99874134.0	E MTAB 9193:cDNA8h 1 S2 L001	0:101	A:2892833391;C:2022466595;G:2198646699;T:2962268446;N:11072403	101		2892833391	2022466595	2198646699	2962268446	11072403	ERX4155254	ERS4601292	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93609	0.12902	0.82158	0.5062	101	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9899	9899	ERR4194115	ERX4155254	ERS4601292	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 2	SAMEA6873729	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873729\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 2\|age:8\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 2\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 2 s	Sample 2 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:8\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA8h_1_S2_L002.bam	bam	10191911414.0	100910014.0	E MTAB 9193:cDNA8h 1 S2 L002	0:101	A:2923216190;C:2043975715;G:2221734566;T:2992798366;N:10186577	101		2923216190	2043975715	2221734566	2992798366	10186577	ERX4155254	ERS4601292	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93445	0.13038	0.824	0.49774	101	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9900	9900	ERR4194112	ERX4155253	ERS4601291	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 1	SAMEA6873728	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873728\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 1\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 1 s	Sample 1 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:6\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA6h_1_S1_L001.bam	bam	7181772357.0	71106657.0	E MTAB 9193:cDNA6h 1 S1 L001	0:101	A:2074032710;C:1415439071;G:1544274166;T:2140112533;N:7913877	101		2074032710	1415439071	1544274166	2140112533	7913877	ERX4155253	ERS4601291	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.9297	0.12156	0.8117	0.51457	101	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9901	9901	ERR4194113	ERX4155253	ERS4601291	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 1	SAMEA6873728	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873728\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 1\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 1 s	Sample 1 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:6\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA6h_1_S1_L002.bam	bam	7256542253.0	71846953.0	E MTAB 9193:cDNA6h 1 S1 L002	0:101	A:2096163385;C:1430325700;G:1560530043;T:2162265616;N:7257509	101		2096163385	1430325700	1560530043	2162265616	7257509	ERX4155253	ERS4601291	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.92882	0.12127	0.81162	0.51457	101	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9902	9902	ERR4194128	ERX4155256	ERS4601294	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 4	SAMEA6873731	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873731\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 4\|age:13\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 4\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 4 s	Sample 4 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:13\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA13h_1_control_S1_L001.bam	bam	10785974123.0	106791823.0	E MTAB 9193:cDNA13h 1 control S1 L001	0:101	A:3007305661;C:2241057062;G:2505494392;T:2986021199;N:46095809	101		3007305661	2241057062	2505494392	2986021199	46095809	ERX4155256	ERS4601294	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.67094	0.07571	0.92951	0.5272	101	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9903	9903	ERR4194129	ERX4155256	ERS4601294	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 4	SAMEA6873731	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873731\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 4\|age:13\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 4\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 4 s	Sample 4 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:13\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA13h_1_control_S1_L002.bam	bam	10595192294.0	104902894.0	E MTAB 9193:cDNA13h 1 control S1 L002	0:101	A:2971916419;C:2204229263;G:2390854035;T:2949877754;N:78314823	101		2971916419	2204229263	2390854035	2949877754	78314823	ERX4155256	ERS4601294	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.67255	0.08054	0.91583	0.52661	101	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9904	9904	ERR4194116	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_1_S3_L001.bam	bam	1622536412.0	16556494.0	E MTAB 9193:cDNA10h 1 S3 L001	0:98	A:491141175;C:317161060;G:354179755;T:459976409;N:78013	98		491141175	317161060	354179755	459976409	78013	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93238	0.13033	0.89132	0.47076	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9905	9905	ERR4194117	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_1_S3_L002.bam	bam	1484328776.0	15146212.0	E MTAB 9193:cDNA10h 1 S3 L002	0:98	A:450782055;C:290088574;G:322801188;T:420570801;N:86158	98		450782055	290088574	322801188	420570801	86158	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.92846	0.13128	0.89923	0.46879	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9906	9906	ERR4194118	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_1_S3_L003.bam	bam	1578833116.0	16110542.0	E MTAB 9193:cDNA10h 1 S3 L003	0:98	A:477600666;C:308260969;G:347303289;T:445467384;N:200808	98		477600666	308260969	347303289	445467384	200808	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93107	0.12965	0.91265	0.47375	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9907	9907	ERR4194119	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_1_S3_L004.bam	bam	1859564994.0	18975153.0	E MTAB 9193:cDNA10h 1 S3 L004	0:98	A:562936790;C:364057256;G:406607636;T:525811595;N:151717	98		562936790	364057256	406607636	525811595	151717	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93453	0.1266	0.87714	0.46957	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9908	9908	ERR4194120	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L001.bam	bam	1156341102.0	11799399.0	E MTAB 9193:cDNA10h 2 S3 L001	0:98	A:345857612;C:224453195;G:257551986;T:327969064;N:509245	98		345857612	224453195	257551986	327969064	509245	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93863	0.10744	0.81984	0.501	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9909	9909	ERR4194121	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L002.bam	bam	1105219696.0	11277752.0	E MTAB 9193:cDNA10h 2 S3 L002	0:98	A:331051973;C:214369903;G:246546338;T:312897773;N:353709	98		331051973	214369903	246546338	312897773	353709	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93941	0.10818	0.82211	0.50079	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9910	9910	ERR4194122	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L003.bam	bam	1105199606.0	11277547.0	E MTAB 9193:cDNA10h 2 S3 L003	0:98	A:331158619;C:214305131;G:246465559;T:312930408;N:339889	98		331158619	214305131	246465559	312930408	339889	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93767	0.10645	0.82329	0.50057	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9911	9911	ERR4194123	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L004.bam	bam	1108707712.0	11313344.0	E MTAB 9193:cDNA10h 2 S3 L004	0:98	A:331374433;C:215925150;G:247131942;T:313865174;N:411013	98		331374433	215925150	247131942	313865174	411013	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93827	0.10842	0.82031	0.49241	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9912	9912	ERR4194124	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L005.bam	bam	1110084612.0	11327394.0	E MTAB 9193:cDNA10h 2 S3 L005	0:98	A:332881960;C:215360330;G:247563319;T:313842331;N:436672	98		332881960	215360330	247563319	313842331	436672	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93827	0.10719	0.8238	0.50406	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9913	9913	ERR4194125	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L006.bam	bam	1113812728.0	11365436.0	E MTAB 9193:cDNA10h 2 S3 L006	0:98	A:333112288;C:216649152;G:248341020;T:315338848;N:371420	98		333112288	216649152	248341020	315338848	371420	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93843	0.10675	0.82079	0.49284	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9914	9914	ERR4194126	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L007.bam	bam	1119495748.0	11423426.0	E MTAB 9193:cDNA10h 2 S3 L007	0:98	A:335288339;C:217283719;G:249624836;T:316900388;N:398466	98		335288339	217283719	249624836	316900388	398466	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93711	0.10749	0.82266	0.49382	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9915	9915	ERR4194127	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L008.bam	bam	1175946688.0	11999456.0	E MTAB 9193:cDNA10h 2 S3 L008	0:98	A:351364169;C:228318193;G:261971072;T:333863943;N:429311	98		351364169	228318193	261971072	333863943	429311	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93851	0.10755	0.82158	0.49895	98	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9916	9916	ERR4194130	ERX4155257	ERS4601295	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 5	SAMEA6873732	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873732\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 5\|age:13\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 5\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 5 s	Sample 5 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:13\|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA13h_2_gata56KD_S2_L001.bam	bam	7791309377.0	77141677.0	E MTAB 9193:cDNA13h 2 gata56KD S2 L001	0:101	A:2198242220;C:1593746618;G:1784167452;T:2181979820;N:33173267	101		2198242220	1593746618	1784167452	2181979820	33173267	ERX4155257	ERS4601295	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.66736	0.08039	0.93026	0.50796	101	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9917	9917	ERR4194131	ERX4155257	ERS4601295	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 5	SAMEA6873732	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873732\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 5\|age:13\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 5\|scientific name:Danio rerio\|sex:mixed	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 5 s	Sample 5 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:13\|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA13h_2_gata56KD_S2_L002.bam	bam	7658149967.0	75823267.0	E MTAB 9193:cDNA13h 2 gata56KD S2 L002	0:101	A:2172230233;C:1568805100;G:1703587704;T:2157181071;N:56345859	101		2172230233	1568805100	1703587704	2157181071	56345859	ERX4155257	ERS4601295	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.66565	0.08597	0.91804	0.51772	101	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
10060	10060	ERR4795364	ERX4665135	ERS5281176	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 4	E MTAB 9727:Sample 4		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 4 s	Sample 4 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz	fastq	5410723202.0	71707309.0	E MTAB 9727:Sample 4	0:75.46 1:0	A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666	75	0	1330416803	531269504	734031980	2814959249	45666	ERX4665135	ERS5281176	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.33614	0.21532	0.99019	0.41002	76	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10061	10061	ERR4795365	ERX4665135	ERS5281176	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 4	E MTAB 9727:Sample 4		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 4 s	Sample 4 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz	fastq	5414184547.0	71707309.0	E MTAB 9727:Sample 4 1	0:0 1:75.50	A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967	0	75	1582938104	1052565419	1177180395	1600161662	1338967	ERX4665135	ERS5281176	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.84976	0.28521	0.85038	0.5124	75	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10062	10062	ERR4795362	ERX4665134	ERS5281175	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 3	E MTAB 9727:Sample 3		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 3 s	Sample 3 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz	fastq	4823193891.0	63965519.0	E MTAB 9727:Sample 3	0:75.40 1:0	A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086	75	0	1323978162	446831209	581746343	2470114091	524086	ERX4665134	ERS5281175	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.36549	0.19722	0.95552	0.4702	76	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10063	10063	ERR4795363	ERX4665134	ERS5281175	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 3	E MTAB 9727:Sample 3		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 3 s	Sample 3 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz	fastq	4828889391.0	63965519.0	E MTAB 9727:Sample 3 1	0:0 1:75.49	A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756	0	75	1434099697	964508763	893584575	1534727600	1968756	ERX4665134	ERS5281175	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.85811	0.26231	0.82731	0.48618	76	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10064	10064	ERR4795360	ERX4665133	ERS5281174	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 2	E MTAB 9727:Sample 2		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 2 s	Sample 2 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz	fastq	5598371393.0	74235388.0	E MTAB 9727:Sample 2	0:75.41 1:0	A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655	75	0	1526486973	558020193	717587491	2795646081	630655	ERX4665133	ERS5281174	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.28059	0.19252	0.96404	0.4874	75	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10065	10065	ERR4795361	ERX4665133	ERS5281174	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 2	E MTAB 9727:Sample 2		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 2 s	Sample 2 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz	fastq	5600151371.0	74235388.0	E MTAB 9727:Sample 2 1	0:0 1:75.44	A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060	0	75	1850568176	1035622971	1071138281	1640475883	2346060	ERX4665133	ERS5281174	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.7679	0.30371	0.82651	0.43401	75	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10066	10066	ERR4795358	ERX4665132	ERS5281173	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 1	E MTAB 9727:Sample 1		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 1 s	Sample 1 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz	fastq	4996502316.0	66258508.0	E MTAB 9727:Sample 1	0:75.41 1:0	A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936	75	0	1330744174	451622042	591151500	2622422664	561936	ERX4665132	ERS5281173	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.29754	0.17671	0.9669	0.45463	75	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10067	10067	ERR4795359	ERX4665132	ERS5281173	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 1	E MTAB 9727:Sample 1		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 1 s	Sample 1 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500	ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz	fastq	4999908389.0	66258508.0	E MTAB 9727:Sample 1 1	0:0 1:75.46	A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512	0	75	1591945117	933968124	986108614	1485824022	2062512	ERX4665132	ERS5281173	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.81333	0.2466	0.83027	0.51572	75	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
35567	35567	SRR32928199	SRX28203119	SRS24552825	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.F01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 6	100	100	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.enzymatic.P01.F01.fq.gz	fastq	800436.0	9529.0	expt2.broad.48.enzymatic.P01.F01.fq.gz	0:84	A:247920;C:168170;G:180799;T:203153;N:394	84		247920	168170	180799	203153	394	SRX28203119	SRS24552825	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35568	35568	SRR32928200	SRX28203118	SRS24552823	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.E01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 5	99	99	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.enzymatic.P01.E01.fq.gz	fastq	496356.0	5909.0	expt2.broad.48.enzymatic.P01.E01.fq.gz	0:84	A:156600;C:99183;G:113282;T:127036;N:255	84		156600	99183	113282	127036	255	SRX28203118	SRS24552823	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35569	35569	SRR32928201	SRX28203117	SRS24552824	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.D01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 4	98	98	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.enzymatic.P01.D01.fq.gz	fastq	2053800.0	24450.0	expt2.broad.48.enzymatic.P01.D01.fq.gz	0:84	A:668634;C:393806;G:431279;T:559022;N:1059	84		668634	393806	431279	559022	1059	SRX28203117	SRS24552824	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35570	35570	SRR32928202	SRX28203116	SRS24552821	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.C01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 3	97	97	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.enzymatic.P01.C01.fq.gz	fastq	2159052.0	25703.0	expt2.broad.48.enzymatic.P01.C01.fq.gz	0:84	A:837784;C:348085;G:463530;T:508544;N:1109	84		837784	348085	463530	508544	1109	SRX28203116	SRS24552821	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35571	35571	SRR32928203	SRX28203115	SRS24552822	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.B01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 2	96	96	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.enzymatic.P01.B01.fq.gz	fastq	3287508.0	39137.0	expt2.broad.48.enzymatic.P01.B01.fq.gz	0:84	A:1090202;C:644484;G:702124;T:848812;N:1886	84		1090202	644484	702124	848812	1886	SRX28203115	SRS24552822	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35572	35572	SRR32928204	SRX28203114	SRS24552819	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.A01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 1	95	95	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.enzymatic.P01.A01.fq.gz	fastq	6623400.0	78850.0	expt2.broad.48.enzymatic.P01.A01.fq.gz	0:84	A:2915935;C:1012732;G:1256523;T:1434621;N:3589	84		2915935	1012732	1256523	1434621	3589	SRX28203114	SRS24552819	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35573	35573	SRR32928205	SRX28203113	SRS24552820	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.H02.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:16\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 16	94	94	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.H02.fq.gz	fastq	18079152.0	215228.0	expt2.broad.48.bead.P18.H02.fq.gz	0:84	A:6013555;C:3409380;G:3853431;T:4793252;N:9534	84		6013555	3409380	3853431	4793252	9534	SRX28203113	SRS24552820	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35574	35574	SRR32928206	SRX28203112	SRS24552818	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.H01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:15\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 15	93	93	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.H01.fq.gz	fastq	13210764.0	157271.0	expt2.broad.48.bead.P18.H01.fq.gz	0:84	A:4207727;C:2577088;G:2821128;T:3597752;N:7069	84		4207727	2577088	2821128	3597752	7069	SRX28203112	SRS24552818	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35575	35575	SRR32928207	SRX28203111	SRS24552817	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.G02.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:14\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 14	92	92	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.G02.fq.gz	fastq	14834736.0	176604.0	expt2.broad.48.bead.P18.G02.fq.gz	0:84	A:5041294;C:2753273;G:3108141;T:3924037;N:7991	84		5041294	2753273	3108141	3924037	7991	SRX28203111	SRS24552817	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35576	35576	SRR32928310	SRX28203110	SRS24552815	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.G12.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 7	212	212	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.enzymatic.P18.G12.fq.gz	fastq	25010412.0	297743.0	expt3.96.enzymatic.P18.G12.fq.gz	0:84	A:10964374;C:4064284;G:5105517;T:4873835;N:2402	84		10964374	4064284	5105517	4873835	2402	SRX28203110	SRS24552815	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35577	35577	SRR32928208	SRX28203109	SRS24552816	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.F12.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 6	211	211	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.enzymatic.P18.F12.fq.gz	fastq	34833876.0	414689.0	expt3.96.enzymatic.P18.F12.fq.gz	0:84	A:15190499;C:5741220;G:7109697;T:6789172;N:3288	84		15190499	5741220	7109697	6789172	3288	SRX28203109	SRS24552816	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35578	35578	SRR32928209	SRX28203108	SRS24552814	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.H3.fq.gz		seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:22\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 22	22	22	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt1.12.bead.P1.H3.fq.gz	fastq	1098724956.0	13080059.0	expt1.12.bead.P1.H3.fq.gz	0:84	A:504518768;C:161484922;G:183535740;T:248983693;N:201833	84		504518768	161484922	183535740	248983693	201833	SRX28203108	SRS24552814	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35579	35579	SRR32928210	SRX28203107	SRS24552812	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.E12.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 5	210	210	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.enzymatic.P18.E12.fq.gz	fastq	27839784.0	331426.0	expt3.96.enzymatic.P18.E12.fq.gz	0:84	A:11930285;C:4560929;G:5811743;T:5534159;N:2668	84		11930285	4560929	5811743	5534159	2668	SRX28203107	SRS24552812	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35580	35580	SRR32928211	SRX28203106	SRS24552811	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.D12.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 4	209	209	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.enzymatic.P18.D12.fq.gz	fastq	27695556.0	329709.0	expt3.96.enzymatic.P18.D12.fq.gz	0:84	A:12091110;C:4491745;G:5609269;T:5500850;N:2582	84		12091110	4491745	5609269	5500850	2582	SRX28203106	SRS24552811	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35581	35581	SRR32928212	SRX28203105	SRS24552813	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.C12.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 3	208	208	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.enzymatic.P18.C12.fq.gz	fastq	24844932.0	295773.0	expt3.96.enzymatic.P18.C12.fq.gz	0:84	A:10700258;C:4111418;G:5035794;T:4994990;N:2472	84		10700258	4111418	5035794	4994990	2472	SRX28203105	SRS24552813	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35582	35582	SRR32928213	SRX28203104	SRS24552810	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.B12.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 2	207	207	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.enzymatic.P18.B12.fq.gz	fastq	10780812.0	128343.0	expt3.96.enzymatic.P18.B12.fq.gz	0:84	A:4635118;C:1860640;G:2120826;T:2163173;N:1055	84		4635118	1860640	2120826	2163173	1055	SRX28203104	SRS24552810	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.33865	0.22704	0.93659	0.55528	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35583	35583	SRR32928214	SRX28203103	SRS24552809	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.A12.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 1	206	206	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.enzymatic.P18.A12.fq.gz	fastq	10534272.0	125408.0	expt3.96.enzymatic.P18.A12.fq.gz	0:84	A:4632079;C:1746502;G:2069269;T:2085448;N:974	84		4632079	1746502	2069269	2085448	974	SRX28203103	SRS24552809	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.33522	0.19264	0.93624	0.50295	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35584	35584	SRR32928215	SRX28203102	SRS24552808	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.H11.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 8	205	205	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.bead.P18.H11.fq.gz	fastq	235038972.0	2798083.0	expt3.96.bead.P18.H11.fq.gz	0:84	A:85855798;C:40354173;G:45974107;T:62832438;N:22456	84		85855798	40354173	45974107	62832438	22456	SRX28203102	SRS24552808	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.61865	0.46937	0.80791	0.46334	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35585	35585	SRR32928216	SRX28203101	SRS24552807	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.G11.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 7	204	204	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.bead.P18.G11.fq.gz	fastq	280436688.0	3338532.0	expt3.96.bead.P18.G11.fq.gz	0:84	A:105066150;C:48021700;G:54614521;T:72707589;N:26728	84		105066150	48021700	54614521	72707589	26728	SRX28203101	SRS24552807	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.59159	0.43599	0.80842	0.46679	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35586	35586	SRR32928217	SRX28203100	SRS24552806	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.F11.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 6	203	203	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.bead.P18.F11.fq.gz	fastq	286313832.0	3408498.0	expt3.96.bead.P18.F11.fq.gz	0:84	A:106784155;C:49395267;G:55919780;T:74187078;N:27552	84		106784155	49395267	55919780	74187078	27552	SRX28203100	SRS24552806	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.60245	0.44424	0.81124	0.48908	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35587	35587	SRR32928218	SRX28203099	SRS24552804	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.E11.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 5	202	202	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.bead.P18.E11.fq.gz	fastq	307881252.0	3665253.0	expt3.96.bead.P18.E11.fq.gz	0:84	A:115701302;C:52449337;G:59620790;T:80080256;N:29567	84		115701302	52449337	59620790	80080256	29567	SRX28203099	SRS24552804	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.5787	0.44122	0.81854	0.50262	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35588	35588	SRR32928219	SRX28203098	SRS24552803	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.D11.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 4	201	201	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.bead.P18.D11.fq.gz	fastq	300632640.0	3578960.0	expt3.96.bead.P18.D11.fq.gz	0:84	A:113779580;C:51205126;G:58283346;T:77335567;N:29021	84		113779580	51205126	58283346	77335567	29021	SRX28203098	SRS24552803	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.57846	0.43882	0.81925	0.50496	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35589	35589	SRR32928220	SRX28203097	SRS24552805	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.G5.fq.gz		seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:21\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 21	21	21	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt1.12.bead.P1.G5.fq.gz	fastq	561441468.0	6683827.0	expt1.12.bead.P1.G5.fq.gz	0:84	A:234940814;C:88191402;G:96728695;T:141478801;N:101756	84		234940814	88191402	96728695	141478801	101756	SRX28203097	SRS24552805	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.50019	0.4034	0.85959	0.49922	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35590	35590	SRR32928221	SRX28203096	SRS24552802	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.A5.fq.gz		seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 3	3	3	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt1.12.bead.P1.A5.fq.gz	fastq	490718256.0	5841884.0	expt1.12.bead.P1.A5.fq.gz	0:84	A:207644706;C:75241234;G:85463387;T:122279492;N:89437	84		207644706	75241234	85463387	122279492	89437	SRX28203096	SRS24552802	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.50293	0.39872	0.85916	0.50964	84	B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35591	35591	SRR32928222	SRX28203095	SRS24552801	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.C11.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 3	200	200	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.bead.P18.C11.fq.gz	fastq	269049312.0	3202968.0	expt3.96.bead.P18.C11.fq.gz	0:84	A:100635643;C:45939296;G:52190404;T:70258145;N:25824	84		100635643	45939296	52190404	70258145	25824	SRX28203095	SRS24552801	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35592	35592	SRR32928223	SRX28203094	SRS24552799	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.B11.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 2	199	199	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.bead.P18.B11.fq.gz	fastq	123292428.0	1467767.0	expt3.96.bead.P18.B11.fq.gz	0:84	A:45529584;C:21218529;G:24007853;T:32524700;N:11762	84		45529584	21218529	24007853	32524700	11762	SRX28203094	SRS24552799	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35593	35593	SRR32928224	SRX28203093	SRS24552800	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.A11.fq.gz		seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 1	198	198	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt3.96.bead.P18.A11.fq.gz	fastq	277357248.0	3301872.0	expt3.96.bead.P18.A11.fq.gz	0:84	A:105979207;C:47015802;G:54386470;T:69949155;N:26614	84		105979207	47015802	54386470	69949155	26614	SRX28203093	SRS24552800	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35594	35594	SRR32928225	SRX28203092	SRS24552798	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.H03.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 8	197	197	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.enzymatic.P01.H03.fq.gz	fastq	3437364.0	40921.0	expt2.deep.72.enzymatic.P01.H03.fq.gz	0:84	A:1374051;C:578097;G:717673;T:766942;N:601	84		1374051	578097	717673	766942	601	SRX28203092	SRS24552798	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35595	35595	SRR32928226	SRX28203091	SRS24552797	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.G03.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 7	196	196	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.enzymatic.P01.G03.fq.gz	fastq	8559096.0	101894.0	expt2.deep.72.enzymatic.P01.G03.fq.gz	0:84	A:3252394;C:1515721;G:1860485;T:1929016;N:1480	84		3252394	1515721	1860485	1929016	1480	SRX28203091	SRS24552797	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35596	35596	SRR32928227	SRX28203090	SRS24552795	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.F03.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 6	195	195	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.enzymatic.P01.F03.fq.gz	fastq	86570988.0	1030607.0	expt2.deep.72.enzymatic.P01.F03.fq.gz	0:84	A:39076701;C:15258279;G:16117195;T:16103299;N:15514	84		39076701	15258279	16117195	16103299	15514	SRX28203090	SRS24552795	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35597	35597	SRR32928228	SRX28203089	SRS24552796	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.E03.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 5	194	194	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.enzymatic.P01.E03.fq.gz	fastq	21496020.0	255905.0	expt2.deep.72.enzymatic.P01.E03.fq.gz	0:84	A:7897723;C:3941227;G:4608642;T:5044562;N:3866	84		7897723	3941227	4608642	5044562	3866	SRX28203089	SRS24552796	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35598	35598	SRR32928229	SRX28203088	SRS24552794	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.D03.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 4	193	193	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.enzymatic.P01.D03.fq.gz	fastq	38955504.0	463756.0	expt2.deep.72.enzymatic.P01.D03.fq.gz	0:84	A:18141798;C:6097971;G:8057753;T:6650850;N:7132	84		18141798	6097971	8057753	6650850	7132	SRX28203088	SRS24552794	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35599	35599	SRR32928230	SRX28203087	SRS24552793	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.C03.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 3	192	192	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.enzymatic.P01.C03.fq.gz	fastq	51870336.0	617504.0	expt2.deep.72.enzymatic.P01.C03.fq.gz	0:84	A:17090212;C:9836274;G:12030231;T:12904330;N:9289	84		17090212	9836274	12030231	12904330	9289	SRX28203087	SRS24552793	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35600	35600	SRR32928231	SRX28203086	SRS24552791	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.B03.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 2	191	191	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.enzymatic.P01.B03.fq.gz	fastq	14069832.0	167498.0	expt2.deep.72.enzymatic.P01.B03.fq.gz	0:84	A:5389848;C:2403134;G:3075076;T:3199255;N:2519	84		5389848	2403134	3075076	3199255	2519	SRX28203086	SRS24552791	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35601	35601	SRR32928232	SRX28203085	SRS24552792	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.G4.fq.gz		seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:20\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 20	20	20	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt1.12.bead.P1.G4.fq.gz	fastq	515444412.0	6136243.0	expt1.12.bead.P1.G4.fq.gz	0:84	A:215225166;C:80082472;G:88915670;T:131127655;N:93449	84		215225166	80082472	88915670	131127655	93449	SRX28203085	SRS24552792	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35602	35602	SRR32928233	SRX28203084	SRS24552790	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.A03.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 1	190	190	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.enzymatic.P01.A03.fq.gz	fastq	218177316.0	2597349.0	expt2.deep.72.enzymatic.P01.A03.fq.gz	0:84	A:102730118;C:32493129;G:39547427;T:43367265;N:39377	84		102730118	32493129	39547427	43367265	39377	SRX28203084	SRS24552790	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35603	35603	SRR32928234	SRX28203083	SRS24552789	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.G01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:13\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 13	91	91	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.G01.fq.gz	fastq	14202468.0	169077.0	expt2.broad.48.bead.P18.G01.fq.gz	0:84	A:4692822;C:2685182;G:2975257;T:3841545;N:7662	84		4692822	2685182	2975257	3841545	7662	SRX28203083	SRS24552789	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35604	35604	SRR32928235	SRX28203082	SRS24552787	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.D3.fq.gz		seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:10\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 10	10	10	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt1.12.bead.P1.D3.fq.gz	fastq	629856780.0	7498295.0	expt1.12.bead.P1.D3.fq.gz	0:84	A:273859568;C:96165073;G:108875157;T:150842309;N:114673	84		273859568	96165073	108875157	150842309	114673	SRX28203082	SRS24552787	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35605	35605	SRR32928236	SRX28203081	SRS24552788	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.F02.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:12\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 12	90	90	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.F02.fq.gz	fastq	16051728.0	191092.0	expt2.broad.48.bead.P18.F02.fq.gz	0:84	A:5221193;C:3079215;G:3420876;T:4321889;N:8555	84		5221193	3079215	3420876	4321889	8555	SRX28203081	SRS24552788	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35606	35606	SRR32928237	SRX28203080	SRS24552786	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.F01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:11\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 11	89	89	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.F01.fq.gz	fastq	19022388.0	226457.0	expt2.broad.48.bead.P18.F01.fq.gz	0:84	A:6375349;C:3646304;G:4032366;T:4958089;N:10280	84		6375349	3646304	4032366	4958089	10280	SRX28203080	SRS24552786	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35607	35607	SRR32928238	SRX28203079	SRS24552785	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.E02.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:10\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 10	88	88	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.E02.fq.gz	fastq	17436720.0	207580.0	expt2.broad.48.bead.P18.E02.fq.gz	0:84	A:5912075;C:3260546;G:3682832;T:4572094;N:9173	84		5912075	3260546	3682832	4572094	9173	SRX28203079	SRS24552785	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35608	35608	SRR32928239	SRX28203078	SRS24552783	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.E01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:9\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 9	87	87	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.E01.fq.gz	fastq	12759768.0	151902.0	expt2.broad.48.bead.P18.E01.fq.gz	0:84	A:4143321;C:2424389;G:2695567;T:3489773;N:6718	84		4143321	2424389	2695567	3489773	6718	SRX28203078	SRS24552783	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35609	35609	SRR32928240	SRX28203077	SRS24552784	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.D02.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 8	86	86	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.D02.fq.gz	fastq	17226132.0	205073.0	expt2.broad.48.bead.P18.D02.fq.gz	0:84	A:5722683;C:3229414;G:3698323;T:4566519;N:9193	84		5722683	3229414	3698323	4566519	9193	SRX28203077	SRS24552784	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35610	35610	SRR32928241	SRX28203076	SRS24552782	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.D01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 7	85	85	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.D01.fq.gz	fastq	14390124.0	171311.0	expt2.broad.48.bead.P18.D01.fq.gz	0:84	A:4584304;C:2823369;G:3092301;T:3882609;N:7541	84		4584304	2823369	3092301	3882609	7541	SRX28203076	SRS24552782	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35611	35611	SRR32928242	SRX28203075	SRS24552781	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.C02.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 6	84	84	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.C02.fq.gz	fastq	18592560.0	221340.0	expt2.broad.48.bead.P18.C02.fq.gz	0:84	A:6370777;C:3468105;G:3988886;T:4754942;N:9850	84		6370777	3468105	3988886	4754942	9850	SRX28203075	SRS24552781	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35612	35612	SRR32928243	SRX28203074	SRS24552780	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.C01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 5	83	83	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.C01.fq.gz	fastq	12557076.0	149489.0	expt2.broad.48.bead.P18.C01.fq.gz	0:84	A:3977371;C:2443832;G:2711905;T:3417301;N:6667	84		3977371	2443832	2711905	3417301	6667	SRX28203074	SRS24552780	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35613	35613	SRR32928244	SRX28203073	SRS24552779	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.B02.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 4	82	82	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.B02.fq.gz	fastq	14289828.0	170117.0	expt2.broad.48.bead.P18.B02.fq.gz	0:84	A:4795697;C:2698305;G:3083373;T:3704963;N:7490	84		4795697	2698305	3083373	3704963	7490	SRX28203073	SRS24552779	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35614	35614	SRR32928245	SRX28203072	SRS24552778	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.B01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 3	81	81	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.B01.fq.gz	fastq	6255144.0	74466.0	expt2.broad.48.bead.P18.B01.fq.gz	0:84	A:1953811;C:1213806;G:1335743;T:1748533;N:3251	84		1953811	1213806	1335743	1748533	3251	SRX28203072	SRS24552778	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35615	35615	SRR32928246	SRX28203071	SRS24552777	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.C5.fq.gz		seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:9\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 9	9	9	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt1.12.bead.P1.C5.fq.gz	fastq	461470968.0	5493702.0	expt1.12.bead.P1.C5.fq.gz	0:84	A:188895160;C:72428601;G:79983141;T:120080226;N:83840	84		188895160	72428601	79983141	120080226	83840	SRX28203071	SRS24552777	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35616	35616	SRR32928247	SRX28203070	SRS24552776	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.A02.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 2	80	80	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.A02.fq.gz	fastq	16441656.0	195734.0	expt2.broad.48.bead.P18.A02.fq.gz	0:84	A:5495147;C:3127531;G:3493145;T:4317176;N:8657	84		5495147	3127531	3493145	4317176	8657	SRX28203070	SRS24552776	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35617	35617	SRR32928248	SRX28203069	SRS24552775	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.A01.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 1	79	79	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.48.bead.P18.A01.fq.gz	fastq	14319564.0	170471.0	expt2.broad.48.bead.P18.A01.fq.gz	0:84	A:4614154;C:2749141;G:3043759;T:3904988;N:7522	84		4614154	2749141	3043759	3904988	7522	SRX28203069	SRS24552775	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35618	35618	SRR32928249	SRX28203068	SRS24552774	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.H05.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 8	78	78	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.24.enzymatic.P01.H05.fq.gz	fastq	9110220.0	108455.0	expt2.broad.24.enzymatic.P01.H05.fq.gz	0:84	A:3384792;C:1565195;G:1973031;T:2182427;N:4775	84		3384792	1565195	1973031	2182427	4775	SRX28203068	SRS24552774	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35619	35619	SRR32928250	SRX28203067	SRS24552773	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.G05.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 7	77	77	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.24.enzymatic.P01.G05.fq.gz	fastq	4093068.0	48727.0	expt2.broad.24.enzymatic.P01.G05.fq.gz	0:84	A:1283703;C:801390;G:874961;T:1130908;N:2106	84		1283703	801390	874961	1130908	2106	SRX28203067	SRS24552773	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35620	35620	SRR32928251	SRX28203066	SRS24552772	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.F05.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 6	76	76	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.24.enzymatic.P01.F05.fq.gz	fastq	15414840.0	183510.0	expt2.broad.24.enzymatic.P01.F05.fq.gz	0:84	A:6868692;C:2274988;G:2950304;T:3312556;N:8300	84		6868692	2274988	2950304	3312556	8300	SRX28203066	SRS24552772	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35621	35621	SRR32928252	SRX28203065	SRS24552771	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.E05.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 5	75	75	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.24.enzymatic.P01.E05.fq.gz	fastq	7552440.0	89910.0	expt2.broad.24.enzymatic.P01.E05.fq.gz	0:84	A:2833004;C:1314546;G:1543833;T:1856906;N:4151	84		2833004	1314546	1543833	1856906	4151	SRX28203065	SRS24552771	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35622	35622	SRR32928253	SRX28203064	SRS24552770	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.D05.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 4	74	74	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.24.enzymatic.P01.D05.fq.gz	fastq	18449592.0	219638.0	expt2.broad.24.enzymatic.P01.D05.fq.gz	0:84	A:8110605;C:2781954;G:3613141;T:3933803;N:10089	84		8110605	2781954	3613141	3933803	10089	SRX28203064	SRS24552770	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35623	35623	SRR32928254	SRX28203063	SRS24552769	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.C05.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 3	73	73	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.24.enzymatic.P01.C05.fq.gz	fastq	5944344.0	70766.0	expt2.broad.24.enzymatic.P01.C05.fq.gz	0:84	A:2038886;C:1067891;G:1274553;T:1559956;N:3058	84		2038886	1067891	1274553	1559956	3058	SRX28203063	SRS24552769	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35624	35624	SRR32928255	SRX28203062	SRS24552768	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.B05.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 2	72	72	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.24.enzymatic.P01.B05.fq.gz	fastq	8608320.0	102480.0	expt2.broad.24.enzymatic.P01.B05.fq.gz	0:84	A:3054837;C:1594241;G:1754868;T:2199803;N:4571	84		3054837	1594241	1754868	2199803	4571	SRX28203062	SRS24552768	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35625	35625	SRR32928256	SRX28203061	SRS24552767	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.A05.fq.gz		seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 1	71	71	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.broad.24.enzymatic.P01.A05.fq.gz	fastq	3979164.0	47371.0	expt2.broad.24.enzymatic.P01.A05.fq.gz	0:84	A:1268971;C:764759;G:844472;T:1098812;N:2150	84		1268971	764759	844472	1098812	2150	SRX28203061	SRS24552767	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35626	35626	SRR32928257	SRX28203060	SRS24552766	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.C4.fq.gz		seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 8	8	8	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt1.12.bead.P1.C4.fq.gz	fastq	451683456.0	5377184.0	expt1.12.bead.P1.C4.fq.gz	0:84	A:188077465;C:71524093;G:79688471;T:112311489;N:81938	84		188077465	71524093	79688471	112311489	81938	SRX28203060	SRS24552766	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35627	35627	SRR32928258	SRX28203059	SRS24552765	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.H05.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:16\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 16	189	189	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.H05.fq.gz	fastq	100072896.0	1191344.0	expt2.deep.72.bead.P18.H05.fq.gz	0:84	A:37670921;C:17233514;G:20449798;T:24701130;N:17533	84		37670921	17233514	20449798	24701130	17533	SRX28203059	SRS24552765	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35628	35628	SRR32928259	SRX28203058	SRS24552764	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.H04.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:15\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 15	188	188	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.H04.fq.gz	fastq	127374408.0	1516362.0	expt2.deep.72.bead.P18.H04.fq.gz	0:84	A:49385711;C:21752310;G:26316853;T:29896958;N:22576	84		49385711	21752310	26316853	29896958	22576	SRX28203058	SRS24552764	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35629	35629	SRR32928260	SRX28203057	SRS24552763	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.G05.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:14\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 14	187	187	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.G05.fq.gz	fastq	118781376.0	1414064.0	expt2.deep.72.bead.P18.G05.fq.gz	0:84	A:46475832;C:19993091;G:24438008;T:27853488;N:20957	84		46475832	19993091	24438008	27853488	20957	SRX28203057	SRS24552763	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35630	35630	SRR32928261	SRX28203056	SRS24552760	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.G04.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:13\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 13	186	186	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.G04.fq.gz	fastq	129283728.0	1539092.0	expt2.deep.72.bead.P18.G04.fq.gz	0:84	A:51256657;C:21906239;G:26113882;T:29984084;N:22866	84		51256657	21906239	26113882	29984084	22866	SRX28203056	SRS24552760	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35631	35631	SRR32928262	SRX28203055	SRS24552761	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.F05.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:12\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 12	185	185	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.F05.fq.gz	fastq	129148404.0	1537481.0	expt2.deep.72.bead.P18.F05.fq.gz	0:84	A:49582957;C:22353347;G:27049287;T:30139940;N:22873	84		49582957	22353347	27049287	30139940	22873	SRX28203055	SRS24552761	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35632	35632	SRR32928263	SRX28203054	SRS24552762	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.F04.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:11\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 11	184	184	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.F04.fq.gz	fastq	150033996.0	1786119.0	expt2.deep.72.bead.P18.F04.fq.gz	0:84	A:58692014;C:25506404;G:31365137;T:34443610;N:26831	84		58692014	25506404	31365137	34443610	26831	SRX28203054	SRS24552762	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35633	35633	SRR32928264	SRX28203053	SRS24552759	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.E05.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:10\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 10	183	183	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.E05.fq.gz	fastq	126694176.0	1508264.0	expt2.deep.72.bead.P18.E05.fq.gz	0:84	A:51627607;C:20422286;G:26199504;T:28422124;N:22655	84		51627607	20422286	26199504	28422124	22655	SRX28203053	SRS24552759	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35634	35634	SRR32928265	SRX28203052	SRS24552758	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.E04.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:9\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 9	182	182	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.E04.fq.gz	fastq	116357388.0	1385207.0	expt2.deep.72.bead.P18.E04.fq.gz	0:84	A:44265643;C:20201353;G:23492981;T:28376788;N:20623	84		44265643	20201353	23492981	28376788	20623	SRX28203052	SRS24552758	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35635	35635	SRR32928266	SRX28203051	SRS24552756	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.D05.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 8	181	181	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.D05.fq.gz	fastq	108267516.0	1288899.0	expt2.deep.72.bead.P18.D05.fq.gz	0:84	A:41225423;C:18528370;G:22265524;T:26229153;N:19046	84		41225423	18528370	22265524	26229153	19046	SRX28203051	SRS24552756	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35636	35636	SRR32928267	SRX28203050	SRS24552757	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.G3.fq.gz		seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:19\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 19	19	19	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt1.12.bead.P1.G3.fq.gz	fastq	615903456.0	7332184.0	expt1.12.bead.P1.G3.fq.gz	0:84	A:262286368;C:93846834;G:105834930;T:153823652;N:111672	84		262286368	93846834	105834930	153823652	111672	SRX28203050	SRS24552757	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35637	35637	SRR32928268	SRX28203049	SRS24552755	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.D04.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 7	180	180	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.D04.fq.gz	fastq	179121432.0	2132398.0	expt2.deep.72.bead.P18.D04.fq.gz	0:84	A:72040384;C:30579403;G:36178369;T:40291119;N:32157	84		72040384	30579403	36178369	40291119	32157	SRX28203049	SRS24552755	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35638	35638	SRR32928269	SRX28203048	SRS24552754	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.C05.fq.gz		seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal	sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 6	179	179	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.			OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522			expt2.deep.72.bead.P18.C05.fq.gz	fastq	127961736.0	1523354.0	expt2.deep.72.bead.P18.C05.fq.gz	0:84	A:51654447;C:20918642;G:25857491;T:29508510;N:22646	84		51654447	20918642	25857491	29508510	22646	SRX28203048	SRS24552754	SRA2104467	University of Washington\|Genome Sciences	University of Washington							B	usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;