metadata: run_metadata: 454 rows where devstage_curation = "Segmentation" and technology = "10x"

454 rows where devstage_curation = "Segmentation" and technology = "10x"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
11769	11769	ERR11758631	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S10_L001_R2_001.fastq.gz Etv2_Traver_S10_L001_R1_001.fastq.gz	fastq fastq	1947733326.0	15458201.0	E MTAB 13196:Etv2 Traver S10 L001	0:28 1:98	A:532150077;C:434208725;G:472140578;T:508906834;N:327112	28	98			532150077	434208725	472140578	508906834	327112	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00677	0.92596	0.00142	0.07895	0.98526	0.85123	0.42802	0.53518	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11770	11770	ERR11758646	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S28_L001_R2_001.fastq.gz Etv2_Traver_S28_L001_R1_001.fastq.gz	fastq fastq	1091426920.0	8801830.0	E MTAB 13196:Etv2 Traver S28 L001	0:26 1:98	A:302665480;C:247712584;G:269795015;T:271081940;N:171901	26	98			302665480	247712584	269795015	271081940	171901	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00585	0.90012	0.00149	0.07225	0.98746	0.84916	0.39007	0.54873	26	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11771	11771	ERR11758602	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S25_L001_R2_001.fastq.gz Etv2_Traver_S25_L001_R1_001.fastq.gz	fastq fastq	983616732.0	7932393.0	E MTAB 13196:Etv2 Traver S25 L001	0:26 1:98	A:272974243;C:222949925;G:242884450;T:244652916;N:155198	26	98			272974243	222949925	242884450	244652916	155198	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00571	0.90139	0.00143	0.07484	0.98756	0.85019	0.40119	0.54977	26	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11772	11772	ERR11758647	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S27_L001_R2_001.fastq.gz Etv2_Traver_S27_L001_R1_001.fastq.gz	fastq fastq	1162223232.0	9372768.0	E MTAB 13196:Etv2 Traver S27 L001	0:26 1:98	A:322910431;C:262934167;G:286614718;T:289578468;N:185448	26	98			322910431	262934167	286614718	289578468	185448	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00563	0.89924	0.00128	0.07464	0.98762	0.85064	0.38525	0.53889	26	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11773	11773	ERR11758634	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S12_L001_R2_001.fastq.gz Etv2_Traver_S12_L001_R1_001.fastq.gz	fastq fastq	1979462268.0	15710018.0	E MTAB 13196:Etv2 Traver S12 L001	0:28 1:98	A:539088187;C:442520328;G:480420115;T:517077908;N:355730	28	98			539088187	442520328	480420115	517077908	355730	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00707	0.9236	0.00137	0.07727	0.98451	0.85021	0.41845	0.56136	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11774	11774	ERR11758642	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S9_L001_R2_001.fastq.gz Etv2_Traver_S9_L001_R1_001.fastq.gz	fastq fastq	1809560214.0	14361589.0	E MTAB 13196:Etv2 Traver S9 L001	0:28 1:98	A:493206820;C:403886293;G:438502430;T:473641472;N:323199	28	98			493206820	403886293	438502430	473641472	323199	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00668	0.92354	0.00141	0.0785	0.98543	0.84938	0.43326	0.52002	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11775	11775	ERR11758623	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S26_L001_R2_001.fastq.gz Etv2_Traver_S26_L001_R1_001.fastq.gz	fastq fastq	1074533780.0	8665595.0	E MTAB 13196:Etv2 Traver S26 L001	0:26 1:98	A:298569273;C:243430874;G:265536499;T:266825982;N:171152	26	98			298569273	243430874	265536499	266825982	171152	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00579	0.90109	0.00136	0.07564	0.98788	0.85017	0.3554	0.54362	26	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11776	11776	ERR11758596	ERX11157719	ERS16172937	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 15s	SAMEA114192244	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192244\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 15s\|age:16.5\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:15 somite stage\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 15s\|scientific name:Danio rerio\|strain:etv2:Kaede									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 15s p	etv2 15s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2_Traver_S11_L001_R2_001.fastq.gz Etv2_Traver_S11_L001_R1_001.fastq.gz	fastq fastq	2167279758.0	17200633.0	E MTAB 13196:Etv2 Traver S11 L001	0:28 1:98	A:591928396;C:482735357;G:524267488;T:567952272;N:396245	28	98			591928396	482735357	524267488	567952272	396245	ERX11157719	ERS16172937	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00635	0.92351	0.00136	0.07835	0.9865	0.85204	0.41521	0.53672	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11789	11789	ERR11758588	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S12_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S12_L005_R1_001.fastq.gz	fastq fastq	970032168.0	7698668.0	E MTAB 13196:drl h2b dendra 22hpf S12 L005	0:28 1:98	A:268176072;C:223973927;G:223251001;T:254545365;N:85803	28	98			268176072	223973927	223251001	254545365	85803	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00525	0.91336	0.00127	0.06812	0.98995	0.85395	0.40891	0.4918	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11790	11790	ERR11758597	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S42_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S42_L001_R1_001.fastq.gz	fastq fastq	716572206.0	5687081.0	E MTAB 13196:drl h2b dendra 22hpf S42 L001	0:28 1:98	A:198614388;C:164584363;G:164633280;T:188663484;N:76691	28	98			198614388	164584363	164633280	188663484	76691	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00366	0.8889	0.00092	0.06467	0.99261	0.84946	0.41353	0.49235	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11791	11791	ERR11758637	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S44_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S44_L001_R1_001.fastq.gz	fastq fastq	481216932.0	3819182.0	E MTAB 13196:drl h2b dendra 22hpf S44 L001	0:28 1:98	A:133704525;C:110630722;G:110586099;T:126246571;N:49015	28	98			133704525	110630722	110586099	126246571	49015	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00352	0.89199	0.00099	0.06481	0.99308	0.85251	0.50101	0.49137	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11792	11792	ERR11758617	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S41_L001_R1_001.fastq.gz drl_h2b-dendra_22hpf_S41_L001_R2_001.fastq.gz	fastq fastq	690504570.0	5480195.0	E MTAB 13196:drl h2b dendra 22hpf S41 L001	0:28 1:98	A:191676994;C:159013582;G:158945690;T:180795403;N:72901	28	98			191676994	159013582	158945690	180795403	72901	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00342	0.89103	0.00091	0.06637	0.99289	0.85196	0.42362	0.49417	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11793	11793	ERR11758627	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S10_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S10_L005_R1_001.fastq.gz	fastq fastq	1443584898.0	11457023.0	E MTAB 13196:drl h2b dendra 22hpf S10 L005	0:28 1:98	A:398056083;C:333283767;G:332935857;T:379178009;N:131182	28	98			398056083	333283767	332935857	379178009	131182	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00494	0.91295	0.00128	0.06617	0.99101	0.84855	0.40479	0.49207	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11794	11794	ERR11758609	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S40_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S40_L001_R1_001.fastq.gz	fastq fastq	139186908.0	1104658.0	E MTAB 13196:drl h2b dendra 22hpf S40 L001	0:28 1:98	A:39986504;C:31169749;G:30838192;T:37121531;N:70932	28	98			39986504	31169749	30838192	37121531	70932	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00113	0.88601	0.00057	0.08145	0.99801	0.89808	0.48148	0.48722	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11795	11795	ERR11758633	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S39_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S39_L001_R1_001.fastq.gz	fastq fastq	226310742.0	1796117.0	E MTAB 13196:drl h2b dendra 22hpf S39 L001	0:28 1:98	A:64619137;C:51094203;G:50285631;T:60191319;N:120452	28	98			64619137	51094203	50285631	60191319	120452	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00116	0.89046	0.00054	0.07999	0.99797	0.89739	0.58119	0.48393	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11796	11796	ERR11758604	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S9_L005_R1_001.fastq.gz drl_h2b-dendra_22hpf_S9_L005_R2_001.fastq.gz	fastq fastq	1419705504.0	11267504.0	E MTAB 13196:drl h2b dendra 22hpf S9 L005	0:28 1:98	A:390831393;C:328833478;G:328344998;T:371567158;N:128477	28	98			390831393	328833478	328344998	371567158	128477	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00519	0.91357	0.00132	0.0668	0.99042	0.84883	0.46254	0.47002	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11797	11797	ERR11758608	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S43_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S43_L001_R1_001.fastq.gz	fastq fastq	744179814.0	5906189.0	E MTAB 13196:drl h2b dendra 22hpf S43 L001	0:28 1:98	A:206745595;C:171274047;G:171089532;T:194990120;N:80520	28	98			206745595	171274047	171089532	194990120	80520	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0033	0.89238	0.00092	0.06573	0.99348	0.85307	0.42184	0.45487	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11798	11798	ERR11758625	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S11_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S11_L005_R1_001.fastq.gz	fastq fastq	1552027554.0	12317679.0	E MTAB 13196:drl h2b dendra 22hpf S11 L005	0:28 1:98	A:428241149;C:359820303;G:356746163;T:407080418;N:139521	28	98			428241149	359820303	356746163	407080418	139521	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00528	0.91344	0.00122	0.06856	0.98946	0.85667	0.46289	0.49059	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11799	11799	ERR11758594	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S37_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S37_L001_R1_001.fastq.gz	fastq fastq	193604292.0	1536542.0	E MTAB 13196:drl h2b dendra 22hpf S37 L001	0:28 1:98	A:55140258;C:43966158;G:43414595;T:50989845;N:93436	28	98			55140258	43966158	43414595	50989845	93436	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00128	0.89527	0.00063	0.07949	0.99774	0.89538	0.424	0.48666	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11800	11800	ERR11758639	ERX11157717	ERS16172935	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 22hpf	SAMEA114192242	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192242\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 22hpf\|age:22\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:22 hpf\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 22hpf\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 22hpf p	drl 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_22hpf_S38_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S38_L001_R1_001.fastq.gz	fastq fastq	226896894.0	1800769.0	E MTAB 13196:drl h2b dendra 22hpf S38 L001	0:28 1:98	A:65107594;C:50761930;G:50291626;T:60619991;N:115753	28	98			65107594	50761930	50291626	60619991	115753	ERX11157717	ERS16172935	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00111	0.88883	0.00057	0.07885	0.99807	0.89412	0.53921	0.47439	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11801	11801	ERR11758636	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S31_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S31_L001_R2_001.fastq.gz	fastq fastq	188521452.0	1496202.0	E MTAB 13196:drl h2b dendra 12somites S31 L001	0:28 1:98	A:54946745;C:39757518;G:41515822;T:52209939;N:91428	28	98			54946745	39757518	41515822	52209939	91428	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00175	0.90844	0.00064	0.15428	0.99636	0.86393	0.39351	0.52017	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11802	11802	ERR11758612	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S35_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S35_L001_R1_001.fastq.gz	fastq fastq	671596632.0	5330132.0	E MTAB 13196:drl h2b dendra 12somites S35 L001	0:28 1:98	A:189747551;C:145545792;G:153208485;T:183026617;N:68187	28	98			189747551	145545792	153208485	183026617	68187	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00594	0.90285	0.00156	0.12933	0.98823	0.80955	0.40956	0.53154	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11803	11803	ERR11758620	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S36_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S36_L001_R1_001.fastq.gz	fastq fastq	456194592.0	3620592.0	E MTAB 13196:drl h2b dendra 12somites S36 L001	0:28 1:98	A:129689128;C:98798602;G:103687645;T:123970211;N:49006	28	98			129689128	98798602	103687645	123970211	49006	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00578	0.90274	0.00162	0.13523	0.98859	0.81917	0.43296	0.52776	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11804	11804	ERR11758607	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S1_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S1_L005_R1_001.fastq.gz	fastq fastq	1313559828.0	10425078.0	E MTAB 13196:drl h2b dendra 12somites S1 L005	0:28 1:98	A:369071579;C:285484861;G:298845646;T:360037984;N:119758	28	98			369071579	285484861	298845646	360037984	119758	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00866	0.92327	0.00213	0.13248	0.98374	0.80846	0.41836	0.52646	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11805	11805	ERR11758621	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S3_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S3_L005_R1_001.fastq.gz	fastq fastq	1400830452.0	11117702.0	E MTAB 13196:drl h2b dendra 12somites S3 L005	0:28 1:98	A:392932148;C:304653102;G:320171450;T:382949722;N:124030	28	98			392932148	304653102	320171450	382949722	124030	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0091	0.92525	0.00221	0.13204	0.98328	0.80683	0.39896	0.52474	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11806	11806	ERR11758615	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S32_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S32_L001_R1_001.fastq.gz	fastq fastq	130164930.0	1033055.0	E MTAB 13196:drl h2b dendra 12somites S32 L001	0:28 1:98	A:38325421;C:27354135;G:28209607;T:36209402;N:66365	28	98			38325421	27354135	28209607	36209402	66365	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00164	0.90364	0.00061	0.16156	0.99651	0.87846	0.37878	0.51845	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11807	11807	ERR11758590	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S34_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S34_L001_R1_001.fastq.gz	fastq fastq	806214402.0	6398527.0	E MTAB 13196:drl h2b dendra 12somites S34 L001	0:28 1:98	A:227716399;C:174839165;G:184278464;T:219297626;N:82748	28	98			227716399	174839165	184278464	219297626	82748	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00622	0.9021	0.00153	0.13047	0.98772	0.80866	0.40065	0.53454	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11808	11808	ERR11758624	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S33_L001_R2_001.fastq.gz drl_h2b-dendra_12somites_S33_L001_R1_001.fastq.gz	fastq fastq	633634974.0	5028849.0	E MTAB 13196:drl h2b dendra 12somites S33 L001	0:28 1:98	A:179249875;C:137201579;G:144307176;T:172806546;N:69798	28	98			179249875	137201579	144307176	172806546	69798	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00585	0.90174	0.00155	0.12966	0.98831	0.80888	0.45862	0.52706	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11809	11809	ERR11758626	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S4_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S4_L005_R1_001.fastq.gz	fastq fastq	927876096.0	7364096.0	E MTAB 13196:drl h2b dendra 12somites S4 L005	0:28 1:98	A:261732233;C:201837729;G:210685660;T:253535088;N:85386	28	98			261732233	201837729	210685660	253535088	85386	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00851	0.92329	0.00197	0.13519	0.98378	0.81665	0.41822	0.52852	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11810	11810	ERR11758632	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S29_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S29_L001_R2_001.fastq.gz	fastq fastq	213074064.0	1691064.0	E MTAB 13196:drl h2b dendra 12somites S29 L001	0:28 1:98	A:62826305;C:44807633;G:46218609;T:59105445;N:116072	28	98			62826305	44807633	46218609	59105445	116072	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00163	0.90265	0.00072	0.1535	0.99701	0.87241	0.47674	0.51858	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11811	11811	ERR11758592	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S2_L005_R2_001.fastq.gz drl_h2b-dendra_12somites_S2_L005_R1_001.fastq.gz	fastq fastq	1647474570.0	13075195.0	E MTAB 13196:drl h2b dendra 12somites S2 L005	0:28 1:98	A:462072903;C:358669639;G:376971859;T:449610611;N:149558	28	98			462072903	358669639	376971859	449610611	149558	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0086	0.92221	0.00193	0.12995	0.98285	0.80275	0.43249	0.52848	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
11812	11812	ERR11758611	ERX11157716	ERS16172934	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01		Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl 12s	SAMEA114192241	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192241\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl 12s\|age:15\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:12 somite stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl 12s\|scientific name:Danio rerio\|strain:drl:H2B Dendra2									Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl 12s p	drl 12s p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_12somites_S30_L001_R1_001.fastq.gz drl_h2b-dendra_12somites_S30_L001_R2_001.fastq.gz	fastq fastq	223279938.0	1772063.0	E MTAB 13196:drl h2b dendra 12somites S30 L001	0:28 1:98	A:64875575;C:47356253;G:49541812;T:61396530;N:109768	28	98			64875575	47356253	49541812	61396530	109768	ERX11157716	ERS16172934	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00168	0.90617	0.00068	0.15194	0.99669	0.86052	0.46907	0.52824	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
25071	25071	SRR25557904	SRX21286761	SRS18536874	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo gpc4 mutant replicate 3	GSM7689215		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo gpc4 mutant replicate 3	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 /	GSM7689215	GSM7689215: Zebrafish 3 somite stage embryo gpc4 mutant replicate 3; Danio rerio; RNA Seq	GSM7689215 r1	GSM7689215	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa10_S9_L001_I1_001.fastq.gz SCa10_S9_L001_R1_001.fastq.gz SCa10_S9_L001_R2_001.fastq.gz	fastq fastq fastq	7658027748.0	60777998.0	GSM7689215 r1	0:8 1:28 2:90	A:1413987220;C:1275616927;G:1518487007;T:1255320720;N:6607946	8	28	90		1413987220	1275616927	1518487007	1255320720	6607946	SRX21286761	SRS18536874	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.9145		0.33826		0.81911		0.55244		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25072	25072	SRR25557907	SRX21286761	SRS18536874	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo gpc4 mutant replicate 3	GSM7689215		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo gpc4 mutant replicate 3	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 /	GSM7689215	GSM7689215: Zebrafish 3 somite stage embryo gpc4 mutant replicate 3; Danio rerio; RNA Seq	GSM7689215 r1	GSM7689215	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa10_S9_L002_I1_001.fastq.gz SCa10_S9_L002_R1_001.fastq.gz SCa10_S9_L002_R2_001.fastq.gz	fastq fastq fastq	7596598338.0	60290463.0	GSM7689215 r2	0:8 1:28 2:90	A:1401793676;C:1260163640;G:1514694946;T:1242930273;N:6559135	8	28	90		1401793676	1260163640	1514694946	1242930273	6559135	SRX21286761	SRS18536874	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.91223		0.33659		0.81951		0.56048		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25073	25073	SRR25557905	SRX21286760	SRS18536873	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 3	GSM7689214		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 3	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 /	GSM7689214	GSM7689214: Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 3; Danio rerio; RNA Seq	GSM7689214 r1	GSM7689214	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa9_S8_L001_I1_001.fastq.gz SCa9_S8_L001_R1_001.fastq.gz SCa9_S8_L001_R2_001.fastq.gz	fastq fastq fastq	7394810598.0	58688973.0	GSM7689214 r1	0:8 1:28 2:90	A:1372485109;C:1236619456;G:1429532688;T:1237003261;N:6367056	8	28	90		1372485109	1236619456	1429532688	1237003261	6367056	SRX21286760	SRS18536873	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.93189		0.35189		0.81428		0.55145		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25074	25074	SRR25557906	SRX21286760	SRS18536873	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 3	GSM7689214		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 3	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 /	GSM7689214	GSM7689214: Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 3; Danio rerio; RNA Seq	GSM7689214 r1	GSM7689214	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa9_S8_L002_R2_001.fastq.gz SCa9_S8_L002_R1_001.fastq.gz SCa9_S8_L002_I1_001.fastq.gz	fastq fastq fastq	7225367562.0	57344187.0	GSM7689214 r2	0:8 1:28 2:90	A:1340045782;C:1204390270;G:1403517431;T:1206776263;N:6247084	8	28	90		1340045782	1204390270	1403517431	1206776263	6247084	SRX21286760	SRS18536873	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.9295		0.35041		0.81282		0.54439		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25075	25075	SRR25557908	SRX21286759	SRS18536872	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo WT replicate 4	GSM7689213		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo WT replicate 4	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT	GSM7689213	GSM7689213: Zebrafish 3 somite stage embryo WT replicate 4; Danio rerio; RNA Seq	GSM7689213 r1	GSM7689213	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa8_S7_L001_I1_001.fastq.gz SCa8_S7_L001_R1_001.fastq.gz SCa8_S7_L001_R2_001.fastq.gz	fastq fastq fastq	6592612824.0	52322324.0	GSM7689213 r1	0:8 1:28 2:90	A:1241317803;C:1077551342;G:1277112813;T:1107365356;N:5661846	8	28	90		1241317803	1077551342	1277112813	1107365356	5661846	SRX21286759	SRS18536872	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.9184		0.33451		0.80257		0.5437		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25076	25076	SRR25557909	SRX21286759	SRS18536872	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo WT replicate 4	GSM7689213		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo WT replicate 4	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT	GSM7689213	GSM7689213: Zebrafish 3 somite stage embryo WT replicate 4; Danio rerio; RNA Seq	GSM7689213 r1	GSM7689213	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa8_S7_L002_I1_001.fastq.gz SCa8_S7_L002_R1_001.fastq.gz SCa8_S7_L002_R2_001.fastq.gz	fastq fastq fastq	6487605684.0	51488934.0	GSM7689213 r2	0:8 1:28 2:90	A:1220716680;C:1056377671;G:1263379115;T:1087919842;N:5610752	8	28	90		1220716680	1056377671	1263379115	1087919842	5610752	SRX21286759	SRS18536872	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.91785		0.33529		0.80491		0.54634		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25077	25077	SRR25557910	SRX21286758	SRS18536871	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo gpc4 mutant replicate 2	GSM7689212		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo gpc4 mutant replicate 2	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 /	GSM7689212	GSM7689212: Zebrafish 3 somite stage embryo gpc4 mutant replicate 2; Danio rerio; RNA Seq	GSM7689212 r1	GSM7689212	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa7_S6_L001_I1_001.fastq.gz SCa7_S6_L001_R1_001.fastq.gz SCa7_S6_L001_R2_001.fastq.gz	fastq fastq fastq	5918765580.0	46974330.0	GSM7689212 r1	0:8 1:28 2:90	A:1147058417;C:950679988;G:1092174732;T:1032696929;N:5079634	8	28	90		1147058417	950679988	1092174732	1032696929	5079634	SRX21286758	SRS18536871	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.92778		0.26942		0.79537		0.52981		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25078	25078	SRR25557911	SRX21286758	SRS18536871	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo gpc4 mutant replicate 2	GSM7689212		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo gpc4 mutant replicate 2	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 /	GSM7689212	GSM7689212: Zebrafish 3 somite stage embryo gpc4 mutant replicate 2; Danio rerio; RNA Seq	GSM7689212 r1	GSM7689212	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa7_S6_L002_I1_001.fastq.gz SCa7_S6_L002_R1_001.fastq.gz SCa7_S6_L002_R2_001.fastq.gz	fastq fastq fastq	5717347146.0	45375771.0	GSM7689212 r2	0:8 1:28 2:90	A:1107424213;C:915978140;G:1058924217;T:996549767;N:4943053	8	28	90		1107424213	915978140	1058924217	996549767	4943053	SRX21286758	SRS18536871	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.92506		0.26728		0.79588		0.53662		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25079	25079	SRR25557912	SRX21286757	SRS18536870	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 2	GSM7689211		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 2	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 /	GSM7689211	GSM7689211: Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 2; Danio rerio; RNA Seq	GSM7689211 r1	GSM7689211	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa6_S5_L001_R2_001.fastq.gz SCa6_S5_L001_R1_001.fastq.gz SCa6_S5_L001_I1_001.fastq.gz	fastq fastq fastq	8343033678.0	66214553.0	GSM7689211 r1	0:8 1:28 2:90	A:1626185961;C:1332473313;G:1514711288;T:1478792229;N:7146979	8	28	90		1626185961	1332473313	1514711288	1478792229	7146979	SRX21286757	SRS18536870	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.93625		0.29484		0.79417		0.53674		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25080	25080	SRR25557913	SRX21286757	SRS18536870	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 2	GSM7689211		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 2	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 /	GSM7689211	GSM7689211: Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 2; Danio rerio; RNA Seq	GSM7689211 r1	GSM7689211	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa6_S5_L002_R2_001.fastq.gz SCa6_S5_L002_R1_001.fastq.gz SCa6_S5_L002_I1_001.fastq.gz	fastq fastq fastq	8105582520.0	64330020.0	GSM7689211 r2	0:8 1:28 2:90	A:1578955735;C:1291320600;G:1476762446;T:1435669327;N:6993692	8	28	90		1578955735	1291320600	1476762446	1435669327	6993692	SRX21286757	SRS18536870	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.93437		0.29086		0.79275		0.53548		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25081	25081	SRR25557914	SRX21286756	SRS18536869	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo WT replicate 3	GSM7689210		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo WT replicate 3	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT	GSM7689210	GSM7689210: Zebrafish 3 somite stage embryo WT replicate 3; Danio rerio; RNA Seq	GSM7689210 r1	GSM7689210	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa5_S4_L001_R2_001.fastq.gz SCa5_S4_L001_R1_001.fastq.gz SCa5_S4_L001_I1_001.fastq.gz	fastq fastq fastq	6281589636.0	49853886.0	GSM7689210 r1	0:8 1:28 2:90	A:1197591410;C:1015900601;G:1209801929;T:1058162701;N:5393099	8	28	90		1197591410	1015900601	1209801929	1058162701	5393099	SRX21286756	SRS18536869	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.92044		0.29971		0.79859		0.54715		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25082	25082	SRR25557915	SRX21286756	SRS18536869	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo WT replicate 3	GSM7689210		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo WT replicate 3	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT	GSM7689210	GSM7689210: Zebrafish 3 somite stage embryo WT replicate 3; Danio rerio; RNA Seq	GSM7689210 r1	GSM7689210	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa5_S4_L002_R2_001.fastq.gz SCa5_S4_L002_R1_001.fastq.gz SCa5_S4_L002_I1_001.fastq.gz	fastq fastq fastq	6214447512.0	49321012.0	GSM7689210 r2	0:8 1:28 2:90	A:1183686671;C:1001370398;G:1203078760;T:1045392607;N:5362644	8	28	90		1183686671	1001370398	1203078760	1045392607	5362644	SRX21286756	SRS18536869	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.9185		0.29684		0.79772		0.54357		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25083	25083	SRR25557916	SRX21286755	SRS18536868	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo gpc4 mutant replicate 1	GSM7689209		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo gpc4 mutant replicate 1	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 /	GSM7689209	GSM7689209: Zebrafish 3 somite stage embryo gpc4 mutant replicate 1; Danio rerio; RNA Seq	GSM7689209 r1	GSM7689209	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa4_S3_L001_I1_001.fastq.gz SCa4_S3_L001_R1_001.fastq.gz SCa4_S3_L001_R2_001.fastq.gz	fastq fastq fastq	7478711100.0	59354850.0	GSM7689209 r1	0:8 1:28 2:90	A:1413795475;C:1224103700;G:1442703432;T:1254915804;N:6418089	8	28	90		1413795475	1224103700	1442703432	1254915804	6418089	SRX21286755	SRS18536868	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.92521		0.27312		0.80028		0.55132		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25084	25084	SRR25557917	SRX21286755	SRS18536868	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo gpc4 mutant replicate 1	GSM7689209		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo gpc4 mutant replicate 1	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:gpc4 /	GSM7689209	GSM7689209: Zebrafish 3 somite stage embryo gpc4 mutant replicate 1; Danio rerio; RNA Seq	GSM7689209 r1	GSM7689209	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa4_S3_L002_I1_001.fastq.gz SCa4_S3_L002_R1_001.fastq.gz SCa4_S3_L002_R2_001.fastq.gz	fastq fastq fastq	7354403154.0	58368279.0	GSM7689209 r2	0:8 1:28 2:90	A:1389352030;C:1199199732;G:1426024579;T:1232220085;N:6348684	8	28	90		1389352030	1199199732	1426024579	1232220085	6348684	SRX21286755	SRS18536868	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.92347		0.27152		0.80271		0.54709		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25085	25085	SRR25557918	SRX21286754	SRS18536867	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 1	GSM7689208		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 1	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 /	GSM7689208	GSM7689208: Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 1; Danio rerio; RNA Seq	GSM7689208 r1	GSM7689208	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa3_S2_L001_I1_001.fastq.gz SCa3_S2_L001_R1_001.fastq.gz SCa3_S2_L001_R2_001.fastq.gz	fastq fastq fastq	7236003222.0	57428597.0	GSM7689208 r1	0:8 1:28 2:90	A:1419674513;C:1150647971;G:1309649875;T:1282359791;N:6241580	8	28	90		1419674513	1150647971	1309649875	1282359791	6241580	SRX21286754	SRS18536867	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.94312		0.22026		0.78859		0.52624		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25086	25086	SRR25557919	SRX21286754	SRS18536867	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 1	GSM7689208		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 / \|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 1	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:dact1 / ;dact2 /	GSM7689208	GSM7689208: Zebrafish 3 somite stage embryo dact1 / ;dact2 / compound mutant replicate 1; Danio rerio; RNA Seq	GSM7689208 r1	GSM7689208	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa3_S2_L002_I1_001.fastq.gz SCa3_S2_L002_R1_001.fastq.gz SCa3_S2_L002_R2_001.fastq.gz	fastq fastq fastq	7120254456.0	56509956.0	GSM7689208 r2	0:8 1:28 2:90	A:1396178983;C:1129610089;G:1293190659;T:1260739942;N:6176367	8	28	90		1396178983	1129610089	1293190659	1260739942	6176367	SRX21286754	SRS18536867	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.94419		0.21971		0.78835		0.53069		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25087	25087	SRR25557920	SRX21286753	SRS18536866	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo WT replicate 2	GSM7689207		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo WT replicate 2	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT	GSM7689207	GSM7689207: Zebrafish 3 somite stage embryo WT replicate 2; Danio rerio; RNA Seq	GSM7689207 r1	GSM7689207	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa2_S1_L001_R2_001.fastq.gz SCa2_S1_L001_R1_001.fastq.gz SCa2_S1_L001_I1_001.fastq.gz	fastq fastq fastq	6465216618.0	51311243.0	GSM7689207 r1	0:8 1:28 2:90	A:1221301953;C:1063429161;G:1251939862;T:1075781853;N:5559041	8	28	90		1221301953	1063429161	1251939862	1075781853	5559041	SRX21286753	SRS18536866	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.92429		0.30596		0.80643		0.55126		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25088	25088	SRR25557921	SRX21286753	SRS18536866	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo WT replicate 2	GSM7689207		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo WT replicate 2	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT	GSM7689207	GSM7689207: Zebrafish 3 somite stage embryo WT replicate 2; Danio rerio; RNA Seq	GSM7689207 r1	GSM7689207	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa2_S1_L002_R2_001.fastq.gz SCa2_S1_L002_R1_001.fastq.gz SCa2_S1_L002_I1_001.fastq.gz	fastq fastq fastq	6329759058.0	50236183.0	GSM7689207 r2	0:8 1:28 2:90	A:1195198147;C:1037452646;G:1231269613;T:1051855332;N:5480732	8	28	90		1195198147	1037452646	1231269613	1051855332	5480732	SRX21286753	SRS18536866	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.92148		0.30109		0.80553		0.53596		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25089	25089	SRR25557922	SRX21286752	SRS18536865	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo WT replicate 1	GSM7689206		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo WT replicate 1	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT	GSM7689206	GSM7689206: Zebrafish 3 somite stage embryo WT replicate 1; Danio rerio; RNA Seq	GSM7689206 r1	GSM7689206	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa1-1_S1_L001_I1_001.fastq.gz SCa1-1_S1_L001_R1_001.fastq.gz SCa1-1_S1_L001_R2_001.fastq.gz	fastq fastq fastq	11794078012.0	92866756.0	GSM7689206 r1	0:8 1:28 2:91	A:2300387451;C:1883840049;G:2243793545;T:2021150417;N:1703334	8	28	91		2300387451	1883840049	2243793545	2021150417	1703334	SRX21286752	SRS18536865	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.90777		0.25227		0.81002		0.55078		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
25090	25090	SRR25557923	SRX21286752	SRS18536865	SRP453890	PRJNA1003061	dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development	GSE240264	Transcriptome Analysis	Wnt signaling plays a fundamental role in the initial patterning and development of the embryo including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled however the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 / zebrafish a convergent extension mutant with an opposite craniofacial phenotype we identified dact1/2 specific roles during early development. Using this subtractive approach we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain capn8 suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT 3 dact1 / ;dact2 / compound mutant and 3 gpc4 / mutant embryos harvested at the 3 somite stage to assess transcriptomic perturbations during development induced by deletion of dact1/2.		pubmed:37986847		Zebrafish 3 somite stage embryo WT replicate 1	GSM7689206		source name:whole embryo\|tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish 3 somite stage embryo WT replicate 1	FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.	whole embryo		Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell 3’ kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit version 3	Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.	tissue:whole embryo\|strain:Tubingen\|developmental stage:3 somite stage\|genotype:WT	GSM7689206	GSM7689206: Zebrafish 3 somite stage embryo WT replicate 1; Danio rerio; RNA Seq	GSM7689206 r1	GSM7689206	1	Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase washed 3x in embryo medium and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation cells were passed through a 70 um cell strainer and cell counts and viability were measured. post droplet encapsulation barcoding and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3 data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation barcoding and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453890		loader:fastq load.py	SCa1-1_S1_L002_I1_001.fastq.gz SCa1-1_S1_L002_R1_001.fastq.gz SCa1-1_S1_L002_R2_001.fastq.gz	fastq fastq fastq	10733970785.0	84519455.0	GSM7689206 r2	0:8 1:28 2:91	A:2105367354;C:1681885566;G:2045327094;T:1857192371;N:1498020	8	28	91		2105367354	1681885566	2045327094	1857192371	1498020	SRX21286752	SRS18536865	SRA1688444	Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health	Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)	1	0.89521		0.23522		0.81947		0.54975		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-07	Segmentation	Embryo	Whole Organism	All anatomical structures
26493	26493	SRR26044865	SRX21761777	SRS18868295	SRP459729	PRJNA1015262	Rtf1 dependent transcriptional pausing regulates cardiogenesis	PRJNA1015262	Other	During heart development an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis we found that Rtf1 is essential for cardiogenesis and that without xxx activity cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain which confers interaction with the pausing/elongation factor Spt5 was required for Rtf1's ability to support cardiac progenitor formation while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced suggesting a reduction in transcriptional pausing. Intriguingly pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.					Rtf1MO single cell Multiome GEX 11 12 somite stage		strain:AB\|age:11 12 somite stage\|collection date:2021 03 10\|geo loc name:USA:California Los Angeles\|sex:n/a\|tissue:whole embryo\|morpholino:rtf1\|assay:GEX\|BioSampleModel:Model organism or animal									10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq	GEX MO	GEX MO	Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729			MO-3GEX_S2_L002_R2_001.fastq.gz MO-3GEX_S2_L002_R1_001.fastq.gz MO-3GEX_S2_L002_I2_001.fastq.gz MO-3GEX_S2_L002_I1_001.fastq.gz MO-3GEX_S2_L001_R2_001.fastq.gz MO-3GEX_S2_L001_R1_001.fastq.gz MO-3GEX_S2_L001_I2_001.fastq.gz MO-3GEX_S2_L001_I1_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	50770012872.0	367898644.0	MO 3GEX S2 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:10123747774;C:6493264924;G:7104700568;T:9387645989;N:1518705	10	10	28	90	10123747774	6493264924	7104700568	9387645989	1518705	SRX21761777	SRS18868295	SRA1710715	University of California, Los Angeles\|Molecular, Cell, and Developmental Biology	University of California, Los Angeles	1	0.87322		0.43479		0.76881		0.57534		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26494	26494	SRR26044866	SRX21761776	SRS18868294	SRP459729	PRJNA1015262	Rtf1 dependent transcriptional pausing regulates cardiogenesis	PRJNA1015262	Other	During heart development an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis we found that Rtf1 is essential for cardiogenesis and that without xxx activity cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain which confers interaction with the pausing/elongation factor Spt5 was required for Rtf1's ability to support cardiac progenitor formation while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced suggesting a reduction in transcriptional pausing. Intriguingly pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.					Control single cell Multiome GEX 11 12 somite stage		strain:AB\|age:11 12 somite stage\|collection date:2021 03 10\|geo loc name:USA:California Los Angeles\|sex:n/a\|tissue:whole embryo\|morpholino:uninjected\|assay:GEX\|BioSampleModel:Model organism or animal									10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq	GEX WT	GEX WT	Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729			WT-3GEX_S1_L001_I1_001.fastq.gz WT-3GEX_S1_L001_I2_001.fastq.gz WT-3GEX_S1_L001_R1_001.fastq.gz WT-3GEX_S1_L001_R2_001.fastq.gz WT-3GEX_S1_L002_I1_001.fastq.gz WT-3GEX_S1_L002_I2_001.fastq.gz WT-3GEX_S1_L002_R1_001.fastq.gz WT-3GEX_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	54878873586.0	397672997.0	WT 3GEX S1 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:10837179080;C:7155333415;G:7765967855;T:10030437304;N:1652076	10	10	28	90	10837179080	7155333415	7765967855	10030437304	1652076	SRX21761776	SRS18868294	SRA1710715	University of California, Los Angeles\|Molecular, Cell, and Developmental Biology	University of California, Los Angeles	1	0.89445		0.37406		0.75481		0.57841		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26495	26495	SRR26044766	SRX21761676	SRS18868295	SRP459729	PRJNA1015262	Rtf1 dependent transcriptional pausing regulates cardiogenesis	PRJNA1015262	Other	During heart development an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis we found that Rtf1 is essential for cardiogenesis and that without xxx activity cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain which confers interaction with the pausing/elongation factor Spt5 was required for Rtf1's ability to support cardiac progenitor formation while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced suggesting a reduction in transcriptional pausing. Intriguingly pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.					Rtf1MO single cell Multiome GEX 11 12 somite stage		strain:AB\|age:11 12 somite stage\|collection date:2021 03 10\|geo loc name:USA:California Los Angeles\|sex:n/a\|tissue:whole embryo\|morpholino:rtf1\|assay:GEX\|BioSampleModel:Model organism or animal									10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq	GEX MO	GEX MO	Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729			MO_3GEX_S2_L004_R2_001.fastq.gz MO_3GEX_S2_L004_R1_001.fastq.gz MO_3GEX_S2_L004_I2_001.fastq.gz MO_3GEX_S2_L004_I1_001.fastq.gz MO_3GEX_S2_L003_R2_001.fastq.gz MO_3GEX_S2_L003_R1_001.fastq.gz MO_3GEX_S2_L003_I2_001.fastq.gz MO_3GEX_S2_L003_I1_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	2914080840.0	13245822.0	MO 3GEX S2 L003 I1 001.fastq.gz	0:10 1:10 2:100 3:100	A:726829083;C:402485666;G:452882760;T:1066890018;N:76873	10	10	100	100	726829083	402485666	452882760	1066890018	76873	SRX21761676	SRS18868295	SRA1710703	University of California, Los Angeles\|Molecular, Cell, and Developmental Biology	University of California, Los Angeles	2	0.22802	0.87048	0.10701	0.42845	0.95595	0.77015	0.60757	0.57362	100	100	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26496	26496	SRR26044767	SRX21761675	SRS18868294	SRP459729	PRJNA1015262	Rtf1 dependent transcriptional pausing regulates cardiogenesis	PRJNA1015262	Other	During heart development an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis we found that Rtf1 is essential for cardiogenesis and that without xxx activity cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain which confers interaction with the pausing/elongation factor Spt5 was required for Rtf1's ability to support cardiac progenitor formation while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced suggesting a reduction in transcriptional pausing. Intriguingly pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.					Control single cell Multiome GEX 11 12 somite stage		strain:AB\|age:11 12 somite stage\|collection date:2021 03 10\|geo loc name:USA:California Los Angeles\|sex:n/a\|tissue:whole embryo\|morpholino:uninjected\|assay:GEX\|BioSampleModel:Model organism or animal									10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq	GEX WT	GEX WT	Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729			WT_3GEX_S1_L004_R2_001.fastq.gz WT_3GEX_S1_L004_R1_001.fastq.gz WT_3GEX_S1_L004_I2_001.fastq.gz WT_3GEX_S1_L004_I1_001.fastq.gz WT_3GEX_S1_L003_R2_001.fastq.gz WT_3GEX_S1_L003_R1_001.fastq.gz WT_3GEX_S1_L003_I2_001.fastq.gz WT_3GEX_S1_L003_I1_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	4986906540.0	22667757.0	WT 3GEX S1 L003 I1 001.fastq.gz	0:10 1:10 2:100 3:100	A:1227427708;C:695004251;G:785531191;T:1825414315;N:173935	10	10	100	100	1227427708	695004251	785531191	1825414315	173935	SRX21761675	SRS18868294	SRA1710703	University of California, Los Angeles\|Molecular, Cell, and Developmental Biology	University of California, Los Angeles	2	0.21872	0.89321	0.09696	0.36976	0.9558	0.75639	0.62213	0.46544	100	100	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26497	26497	SRR26044613	SRX21761588	SRS18868295	SRP459729	PRJNA1015262	Rtf1 dependent transcriptional pausing regulates cardiogenesis	PRJNA1015262	Other	During heart development an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis we found that Rtf1 is essential for cardiogenesis and that without xxx activity cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain which confers interaction with the pausing/elongation factor Spt5 was required for Rtf1's ability to support cardiac progenitor formation while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced suggesting a reduction in transcriptional pausing. Intriguingly pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.					Rtf1MO single cell Multiome GEX 11 12 somite stage		strain:AB\|age:11 12 somite stage\|collection date:2021 03 10\|geo loc name:USA:California Los Angeles\|sex:n/a\|tissue:whole embryo\|morpholino:rtf1\|assay:GEX\|BioSampleModel:Model organism or animal									10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq	GEX MO	GEX MO	Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729			MO_3GEX_S2_L002_R2_001.fastq.gz MO_3GEX_S2_L002_R1_001.fastq.gz MO_3GEX_S2_L002_I2_001.fastq.gz MO_3GEX_S2_L002_I1_001.fastq.gz MO_3GEX_S2_L001_R2_001.fastq.gz MO_3GEX_S2_L001_R1_001.fastq.gz MO_3GEX_S2_L001_I2_001.fastq.gz MO_3GEX_S2_L001_I1_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	21527638854.0	155997383.0	MO 3GEX S2 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:4285470476;C:2755587559;G:3034249420;T:3964137056;N:319959	10	10	28	90	4285470476	2755587559	3034249420	3964137056	319959	SRX21761588	SRS18868295	SRA1710658	University of California, Los Angeles\|Molecular, Cell, and Developmental Biology	University of California, Los Angeles	1	0.87277		0.43202		0.7725		0.56861		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26498	26498	SRR26044614	SRX21761587	SRS18868294	SRP459729	PRJNA1015262	Rtf1 dependent transcriptional pausing regulates cardiogenesis	PRJNA1015262	Other	During heart development an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis we found that Rtf1 is essential for cardiogenesis and that without xxx activity cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain which confers interaction with the pausing/elongation factor Spt5 was required for Rtf1's ability to support cardiac progenitor formation while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced suggesting a reduction in transcriptional pausing. Intriguingly pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.					Control single cell Multiome GEX 11 12 somite stage		strain:AB\|age:11 12 somite stage\|collection date:2021 03 10\|geo loc name:USA:California Los Angeles\|sex:n/a\|tissue:whole embryo\|morpholino:uninjected\|assay:GEX\|BioSampleModel:Model organism or animal									10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq	GEX WT	GEX WT	Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729			WT_3GEX_S1_L001_I1_001.fastq.gz WT_3GEX_S1_L001_I2_001.fastq.gz WT_3GEX_S1_L001_R1_001.fastq.gz WT_3GEX_S1_L001_R2_001.fastq.gz WT_3GEX_S1_L002_I1_001.fastq.gz WT_3GEX_S1_L002_I2_001.fastq.gz WT_3GEX_S1_L002_R1_001.fastq.gz WT_3GEX_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	24359922978.0	176521181.0	WT 3GEX S1 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:4802729436;C:3179460152;G:3468651943;T:4435697892;N:366867	10	10	28	90	4802729436	3179460152	3468651943	4435697892	366867	SRX21761587	SRS18868294	SRA1710658	University of California, Los Angeles\|Molecular, Cell, and Developmental Biology	University of California, Los Angeles	1	0.89475		0.37342		0.75668		0.45872		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
29031	29031	SRR26989303	SRX22682429	SRS19676381	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected stag2b NZ207 scRNA seq	GSM7923481		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207\|geo loc name:missing\|collection date:missing	TB dissected stag2b NZ207 scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207	GSM7923481	GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq	GSM7923481 r1	GSM7923481	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	S2B_bamtofastq_S1_L003_I1_001.fastq.gz S2B_bamtofastq_S1_L003_R1_001.fastq.gz S2B_bamtofastq_S1_L003_R2_001.fastq.gz	fastq fastq fastq	31750000000.0	250000000.0	GSM7923481 r1	0:8 1:28 2:91	A:6537438301;C:4417903496;G:5047922141;T:6745922724;N:813338	8	28	91		6537438301	4417903496	5047922141	6745922724	813338	SRX22682429	SRS19676381	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.93608		0.14792		0.92462		0.51672		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29032	29032	SRR26989304	SRX22682429	SRS19676381	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected stag2b NZ207 scRNA seq	GSM7923481		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207\|geo loc name:missing\|collection date:missing	TB dissected stag2b NZ207 scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207	GSM7923481	GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq	GSM7923481 r1	GSM7923481	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	S2B_bamtofastq_S1_L003_I1_002.fastq.gz S2B_bamtofastq_S1_L003_R1_002.fastq.gz S2B_bamtofastq_S1_L003_R2_002.fastq.gz	fastq fastq fastq	31750000000.0	250000000.0	GSM7923481 r2	0:8 1:28 2:91	A:6518388158;C:4725153194;G:5205254633;T:6300375689;N:828326	8	28	91		6518388158	4725153194	5205254633	6300375689	828326	SRX22682429	SRS19676381	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.95154		0.12683		0.92429		0.45021		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29033	29033	SRR26989305	SRX22682429	SRS19676381	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected stag2b NZ207 scRNA seq	GSM7923481		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207\|geo loc name:missing\|collection date:missing	TB dissected stag2b NZ207 scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207	GSM7923481	GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq	GSM7923481 r1	GSM7923481	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	S2B_bamtofastq_S1_L003_I1_003.fastq.gz S2B_bamtofastq_S1_L003_R1_003.fastq.gz S2B_bamtofastq_S1_L003_R2_003.fastq.gz	fastq fastq fastq	31750000000.0	250000000.0	GSM7923481 r3	0:8 1:28 2:91	A:6383119961;C:4804063495;G:5444337911;T:6117664552;N:814081	8	28	91		6383119961	4804063495	5444337911	6117664552	814081	SRX22682429	SRS19676381	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.94222		0.11028		0.93052		0.61281		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29034	29034	SRR26989306	SRX22682429	SRS19676381	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected stag2b NZ207 scRNA seq	GSM7923481		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207\|geo loc name:missing\|collection date:missing	TB dissected stag2b NZ207 scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207	GSM7923481	GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq	GSM7923481 r1	GSM7923481	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	S2B_bamtofastq_S1_L003_I1_004.fastq.gz S2B_bamtofastq_S1_L003_R1_004.fastq.gz S2B_bamtofastq_S1_L003_R2_004.fastq.gz	fastq fastq fastq	31750000000.0	250000000.0	GSM7923481 r4	0:8 1:28 2:91	A:6402125828;C:4842822163;G:5314139669;T:6190088524;N:823816	8	28	91		6402125828	4842822163	5314139669	6190088524	823816	SRX22682429	SRS19676381	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.94588		0.13163		0.91747		0.45552		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29035	29035	SRR26989307	SRX22682429	SRS19676381	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected stag2b NZ207 scRNA seq	GSM7923481		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207\|geo loc name:missing\|collection date:missing	TB dissected stag2b NZ207 scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:stag2b NZ207	GSM7923481	GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq	GSM7923481 r1	GSM7923481	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	S2B_bamtofastq_S1_L003_I1_005.fastq.gz S2B_bamtofastq_S1_L003_R1_005.fastq.gz S2B_bamtofastq_S1_L003_R2_005.fastq.gz	fastq fastq fastq	21091269095.0	166072985.0	GSM7923481 r5	0:8 1:28 2:91	A:4762107201;C:2885106776;G:3288050363;T:4175805779;N:1571516	8	28	91		4762107201	2885106776	3288050363	4175805779	1571516	SRX22682429	SRS19676381	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.85155		0.18636		0.94314		0.62392		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29036	29036	SRR26989308	SRX22682428	SRS19676380	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected wild type scRNA seq	GSM7923480		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:AB wild type\|geo loc name:missing\|collection date:missing	TB dissected wild type scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:AB wild type	GSM7923480	GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq	GSM7923480 r1	GSM7923480	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	WT_bamtofastq_S1_L003_I1_001.fastq.gz WT_bamtofastq_S1_L003_R1_001.fastq.gz WT_bamtofastq_S1_L003_R2_001.fastq.gz	fastq fastq fastq	31750000000.0	250000000.0	GSM7923480 r1	0:8 1:28 2:91	A:6487643595;C:4511110883;G:5076824945;T:6673593696;N:826881	8	28	91		6487643595	4511110883	5076824945	6673593696	826881	SRX22682428	SRS19676380	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.95134		0.14233		0.91816		0.48251		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29037	29037	SRR26989309	SRX22682428	SRS19676380	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected wild type scRNA seq	GSM7923480		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:AB wild type\|geo loc name:missing\|collection date:missing	TB dissected wild type scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:AB wild type	GSM7923480	GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq	GSM7923480 r1	GSM7923480	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	WT_bamtofastq_S1_L003_I1_002.fastq.gz WT_bamtofastq_S1_L003_R1_002.fastq.gz WT_bamtofastq_S1_L003_R2_002.fastq.gz	fastq fastq fastq	31750000000.0	250000000.0	GSM7923480 r2	0:8 1:28 2:91	A:6572631256;C:4794881740;G:5255235646;T:6126414633;N:836725	8	28	91		6572631256	4794881740	5255235646	6126414633	836725	SRX22682428	SRS19676380	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.96222		0.11199		0.92332		0.50319		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29038	29038	SRR26989310	SRX22682428	SRS19676380	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected wild type scRNA seq	GSM7923480		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:AB wild type\|geo loc name:missing\|collection date:missing	TB dissected wild type scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:AB wild type	GSM7923480	GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq	GSM7923480 r1	GSM7923480	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	WT_bamtofastq_S1_L003_I1_003.fastq.gz WT_bamtofastq_S1_L003_R1_003.fastq.gz WT_bamtofastq_S1_L003_R2_003.fastq.gz	fastq fastq fastq	31750000000.0	250000000.0	GSM7923480 r3	0:8 1:28 2:91	A:6367741226;C:4801321001;G:5377991533;T:6202112567;N:833673	8	28	91		6367741226	4801321001	5377991533	6202112567	833673	SRX22682428	SRS19676380	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.95193		0.10884		0.91362		0.55405		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29039	29039	SRR26989311	SRX22682428	SRS19676380	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected wild type scRNA seq	GSM7923480		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:AB wild type\|geo loc name:missing\|collection date:missing	TB dissected wild type scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:AB wild type	GSM7923480	GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq	GSM7923480 r1	GSM7923480	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	WT_bamtofastq_S1_L003_I1_004.fastq.gz WT_bamtofastq_S1_L003_R1_004.fastq.gz WT_bamtofastq_S1_L003_R2_004.fastq.gz	fastq fastq fastq	31750000000.0	250000000.0	GSM7923480 r4	0:8 1:28 2:91	A:6643013514;C:4783035829;G:5148972841;T:6173682231;N:1295585	8	28	91		6643013514	4783035829	5148972841	6173682231	1295585	SRX22682428	SRS19676380	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.9356		0.12122		0.92084		0.52901		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29040	29040	SRR26989312	SRX22682428	SRS19676380	SRP474934	PRJNA1046494	Cohesin composition and dosage independently affect early development in zebrafish	GSE248952	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		pubmed:38975838		TB dissected wild type scRNA seq	GSM7923480		source name:tailbud\|tissue:tailbud\|age:16 hpf\|genotype:AB wild type\|geo loc name:missing\|collection date:missing	TB dissected wild type scRNA seq	FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files	tailbud		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.		tissue:tailbud\|age:16 hpf\|genotype:AB wild type	GSM7923480	GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq	GSM7923480 r1	GSM7923480	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP474934		loader:fastq load.py	WT_bamtofastq_S1_L003_I1_005.fastq.gz WT_bamtofastq_S1_L003_R1_005.fastq.gz WT_bamtofastq_S1_L003_R2_005.fastq.gz	fastq fastq fastq	3129498186.0	24641718.0	GSM7923480 r5	0:8 1:28 2:91	A:797078402;C:362323092;G:517613944;T:564921437;N:459463	8	28	91		797078402	362323092	517613944	564921437	459463	SRX22682428	SRS19676380	SRA1760034	Chromosome structure and development group, Pathology, University of Otago	Chromosome structure and development group, Pathology, University of Otago	1	0.65184		0.40446		0.95262		0.62704		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	New Zealand	2023-11-29	Segmentation	Embryo	Tail	Multi-system
29457	29457	SRR27352074	SRX23028817	SRS19990700	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1+atf6+creb3l2+creb3l1 cr rep2	GSM7992586		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant\|geo loc name:missing\|collection date:missing	xbp1+atf6+creb3l2+creb3l1 cr rep2	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant	GSM7992586	GSM7992586: xbp1+atf6+creb3l2+creb3l1 cr rep2; Danio rerio; RNA Seq	GSM7992586 r1	GSM7992586	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_8_S1_L001_I1_001.fastq.gz CR_B_8_S1_L001_R1_001.fastq.gz CR_B_8_S1_L001_R2_001.fastq.gz	fastq fastq fastq	8100321390.0	64288265.0	GSM7992586 r1	0:8 1:28 2:90	A:1637929701;C:1240750137;G:1362474512;T:1544230708;N:558792	8	28	90		1637929701	1240750137	1362474512	1544230708	558792	SRX23028817	SRS19990700	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93934		0.13731		0.78668		0.51955		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29458	29458	SRR27352075	SRX23028817	SRS19990700	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1+atf6+creb3l2+creb3l1 cr rep2	GSM7992586		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant\|geo loc name:missing\|collection date:missing	xbp1+atf6+creb3l2+creb3l1 cr rep2	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant	GSM7992586	GSM7992586: xbp1+atf6+creb3l2+creb3l1 cr rep2; Danio rerio; RNA Seq	GSM7992586 r1	GSM7992586	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_8_S2_L004_I1_001.fastq.gz CR_B_8_S2_L004_R1_001.fastq.gz CR_B_8_S2_L004_R2_001.fastq.gz	fastq fastq fastq	22954113210.0	109305301.0	GSM7992586 r2	0:8 1:101 2:101	A:6092285623;C:4225084294;G:4306253605;T:7454948604;N:1098676	8	101	101		6092285623	4225084294	4306253605	7454948604	1098676	SRX23028817	SRS19990700	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.93783	0.0	0.13586	1.0	0.78942		0.52478	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29459	29459	SRR27352076	SRX23028816	SRS19990699	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1+atf6+creb3l2+creb3l1 cr rep1	GSM7992585		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant\|geo loc name:missing\|collection date:missing	xbp1+atf6+creb3l2+creb3l1 cr rep1	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant	GSM7992585	GSM7992585: xbp1+atf6+creb3l2+creb3l1 cr rep1; Danio rerio; RNA Seq	GSM7992585 r1	GSM7992585	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_7_S10_L004_I1_001.fastq.gz CR_B_7_S10_L004_R1_001.fastq.gz CR_B_7_S10_L004_R2_001.fastq.gz	fastq fastq fastq	29069720190.0	138427239.0	GSM7992585 r1	0:8 1:101 2:101	A:7783495559;C:5221642609;G:5386739501;T:9569037022;N:1387587	8	101	101		7783495559	5221642609	5386739501	9569037022	1387587	SRX23028816	SRS19990699	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.92111	0.0	0.14113	1.0	0.79448		0.51334	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29460	29460	SRR27352077	SRX23028816	SRS19990699	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1+atf6+creb3l2+creb3l1 cr rep1	GSM7992585		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant\|geo loc name:missing\|collection date:missing	xbp1+atf6+creb3l2+creb3l1 cr rep1	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant	GSM7992585	GSM7992585: xbp1+atf6+creb3l2+creb3l1 cr rep1; Danio rerio; RNA Seq	GSM7992585 r1	GSM7992585	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_7_S9_L001_I1_001.fastq.gz CR_B_7_S9_L001_R1_001.fastq.gz CR_B_7_S9_L001_R2_001.fastq.gz	fastq fastq fastq	5508123390.0	43715265.0	GSM7992585 r2	0:8 1:28 2:90	A:1133333304;C:826918758;G:919582009;T:1054173491;N:366288	8	28	90		1133333304	826918758	919582009	1054173491	366288	SRX23028816	SRS19990699	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.92229		0.14165		0.79143		0.52513		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29461	29461	SRR27352078	SRX23028815	SRS19990698	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1+creb3l2+creb3l1 cr	GSM7992584		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+creb3l2 double crispant in creb3l1 mutant\|geo loc name:missing\|collection date:missing	xbp1+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+creb3l2 double crispant in creb3l1 mutant	GSM7992584	GSM7992584: xbp1+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992584 r1	GSM7992584	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_6_S15_L001_I1_001.fastq.gz CR_B_6_S15_L001_R1_001.fastq.gz CR_B_6_S15_L001_R2_001.fastq.gz	fastq fastq fastq	14353396596.0	113915846.0	GSM7992584 r1	0:8 1:28 2:90	A:2909860953;C:2217815284;G:2479517248;T:2644258344;N:974311	8	28	90		2909860953	2217815284	2479517248	2644258344	974311	SRX23028815	SRS19990698	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.91818		0.12925		0.80196		0.51684		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29462	29462	SRR27352079	SRX23028815	SRS19990698	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1+creb3l2+creb3l1 cr	GSM7992584		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+creb3l2 double crispant in creb3l1 mutant\|geo loc name:missing\|collection date:missing	xbp1+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+creb3l2 double crispant in creb3l1 mutant	GSM7992584	GSM7992584: xbp1+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992584 r1	GSM7992584	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_6_S17_L004_R2_001.fastq.gz CR_B_6_S17_L004_R1_001.fastq.gz CR_B_6_S17_L004_I1_001.fastq.gz	fastq fastq fastq	25099604250.0	119521925.0	GSM7992584 r2	0:8 1:101 2:101	A:6668848180;C:4658967015;G:4791531572;T:8022877841;N:1204242	8	101	101		6668848180	4658967015	4791531572	8022877841	1204242	SRX23028815	SRS19990698	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.91879	0.0	0.13016	1.0	0.80066		0.52592	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29463	29463	SRR27352080	SRX23028814	SRS19990697	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		creb3l1 cr	GSM7992583		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:creb3l1 crispant\|geo loc name:missing\|collection date:missing	creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:creb3l1 crispant	GSM7992583	GSM7992583: creb3l1 cr; Danio rerio; RNA Seq	GSM7992583 r1	GSM7992583	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_5_S16_L001_I1_001.fastq.gz CR_B_5_S16_L001_R1_001.fastq.gz CR_B_5_S16_L001_R2_001.fastq.gz	fastq fastq fastq	6958012950.0	55222325.0	GSM7992583 r1	0:8 1:28 2:90	A:1403426625;C:1084994842;G:1211813336;T:1269295032;N:479415	8	28	90		1403426625	1084994842	1211813336	1269295032	479415	SRX23028814	SRS19990697	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.90989		0.14602		0.80125		0.54395		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29464	29464	SRR27352081	SRX23028814	SRS19990697	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		creb3l1 cr	GSM7992583		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:creb3l1 crispant\|geo loc name:missing\|collection date:missing	creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:creb3l1 crispant	GSM7992583	GSM7992583: creb3l1 cr; Danio rerio; RNA Seq	GSM7992583 r1	GSM7992583	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_5_S18_L004_I1_001.fastq.gz CR_B_5_S18_L004_R1_001.fastq.gz CR_B_5_S18_L004_R2_001.fastq.gz	fastq fastq fastq	30825792060.0	146789486.0	GSM7992583 r2	0:8 1:101 2:101	A:8136415660;C:5847186555;G:5968579426;T:9697819661;N:1474870	8	101	101		8136415660	5847186555	5968579426	9697819661	1474870	SRX23028814	SRS19990697	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.91089	0.0	0.14577	1.0	0.80545		0.54362	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29465	29465	SRR27352082	SRX23028813	SRS19990696	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		creb3l1 hom rep2	GSM7992582		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:creb3l1 homozygous mutant\|geo loc name:missing\|collection date:missing	creb3l1 hom rep2	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:creb3l1 homozygous mutant	GSM7992582	GSM7992582: creb3l1 hom rep2; Danio rerio; RNA Seq	GSM7992582 r1	GSM7992582	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_4_S10_L001_I1_001.fastq.gz CR_B_4_S10_L001_R1_001.fastq.gz CR_B_4_S10_L001_R2_001.fastq.gz	fastq fastq fastq	24452169840.0	194064840.0	GSM7992582 r1	0:8 1:28 2:90	A:5044437150;C:3614635352;G:4040735660;T:4764365227;N:1662211	8	28	90		5044437150	3614635352	4040735660	4764365227	1662211	SRX23028813	SRS19990696	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.91682		0.14364		0.79377		0.51846		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29466	29466	SRR27352083	SRX23028813	SRS19990696	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		creb3l1 hom rep2	GSM7992582		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:creb3l1 homozygous mutant\|geo loc name:missing\|collection date:missing	creb3l1 hom rep2	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:creb3l1 homozygous mutant	GSM7992582	GSM7992582: creb3l1 hom rep2; Danio rerio; RNA Seq	GSM7992582 r1	GSM7992582	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_4_S11_L004_I1_001.fastq.gz CR_B_4_S11_L004_R1_001.fastq.gz CR_B_4_S11_L004_R2_001.fastq.gz	fastq fastq fastq	35804194230.0	170496163.0	GSM7992582 r2	0:8 1:101 2:101	A:9670502087;C:6331333890;G:6519446707;T:11917229979;N:1712263	8	101	101		9670502087	6331333890	6519446707	11917229979	1712263	SRX23028813	SRS19990696	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.9159	0.0	0.14435	1.0	0.79602		0.51204	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29467	29467	SRR27352084	SRX23028812	SRS19990695	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		tlab rep2	GSM7992581		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:uninjected wild type\|geo loc name:missing\|collection date:missing	tlab rep2	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:uninjected wild type	GSM7992581	GSM7992581: tlab rep2; Danio rerio; RNA Seq	GSM7992581 r1	GSM7992581	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_3_S2_L001_I1_001.fastq.gz CR_B_3_S2_L001_R1_001.fastq.gz CR_B_3_S2_L001_R2_001.fastq.gz	fastq fastq fastq	7414085322.0	58841947.0	GSM7992581 r1	0:8 1:28 2:90	A:1509088988;C:1122509076;G:1235774536;T:1427895577;N:507053	8	28	90		1509088988	1122509076	1235774536	1427895577	507053	SRX23028812	SRS19990695	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93561		0.12415		0.79245		0.5193		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29468	29468	SRR27352085	SRX23028812	SRS19990695	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		tlab rep2	GSM7992581		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:uninjected wild type\|geo loc name:missing\|collection date:missing	tlab rep2	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:uninjected wild type	GSM7992581	GSM7992581: tlab rep2; Danio rerio; RNA Seq	GSM7992581 r1	GSM7992581	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_3_S3_L004_I1_001.fastq.gz CR_B_3_S3_L004_R1_001.fastq.gz CR_B_3_S3_L004_R2_001.fastq.gz	fastq fastq fastq	29102143140.0	138581634.0	GSM7992581 r2	0:8 1:101 2:101	A:7772364211;C:5241576890;G:5378355685;T:9599801424;N:1391858	8	101	101		7772364211	5241576890	5378355685	9599801424	1391858	SRX23028812	SRS19990695	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.93324	0.0	0.1258	1.0	0.79366		0.51785	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29469	29469	SRR27352086	SRX23028811	SRS19990694	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		tlab rep1	GSM7992580		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:uninjected wild type\|geo loc name:missing\|collection date:missing	tlab rep1	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:uninjected wild type	GSM7992580	GSM7992580: tlab rep1; Danio rerio; RNA Seq	GSM7992580 r1	GSM7992580	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_2_S14_L001_I1_001.fastq.gz CR_B_2_S14_L001_R1_001.fastq.gz CR_B_2_S14_L001_R2_001.fastq.gz	fastq fastq fastq	7858063332.0	62365582.0	GSM7992580 r1	0:8 1:28 2:90	A:1610043441;C:1199282341;G:1320931162;T:1482117036;N:528400	8	28	90		1610043441	1199282341	1320931162	1482117036	528400	SRX23028811	SRS19990694	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.92475		0.14694		0.79539		0.51992		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29470	29470	SRR27352087	SRX23028811	SRS19990694	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		tlab rep1	GSM7992580		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:uninjected wild type\|geo loc name:missing\|collection date:missing	tlab rep1	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:uninjected wild type	GSM7992580	GSM7992580: tlab rep1; Danio rerio; RNA Seq	GSM7992580 r1	GSM7992580	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_2_S15_L004_I1_001.fastq.gz CR_B_2_S15_L004_R1_001.fastq.gz CR_B_2_S15_L004_R2_001.fastq.gz	fastq fastq fastq	28374356850.0	135115985.0	GSM7992580 r2	0:8 1:101 2:101	A:7533869602;C:5186086747;G:5306967829;T:9265149451;N:1355341	8	101	101		7533869602	5186086747	5306967829	9265149451	1355341	SRX23028811	SRS19990694	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.92304	0.0	0.14953	1.0	0.79839		0.52679	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29471	29471	SRR27352088	SRX23028810	SRS19990693	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		tyr cr rep2	GSM7992579		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:tyr crispant\|geo loc name:missing\|collection date:missing	tyr cr rep2	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:tyr crispant	GSM7992579	GSM7992579: tyr cr rep2; Danio rerio; RNA Seq	GSM7992579 r1	GSM7992579	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_1_S3_L001_I1_001.fastq.gz CR_B_1_S3_L001_R1_001.fastq.gz CR_B_1_S3_L001_R2_001.fastq.gz	fastq fastq fastq	26329300200.0	208962700.0	GSM7992579 r1	0:8 1:28 2:90	A:5346913205;C:4012936255;G:4434153187;T:5010826566;N:1813787	8	28	90		5346913205	4012936255	4434153187	5010826566	1813787	SRX23028810	SRS19990693	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93538		0.11567		0.78687		0.51206		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29472	29472	SRR27352089	SRX23028810	SRS19990693	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		tyr cr rep2	GSM7992579		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:tyr crispant\|geo loc name:missing\|collection date:missing	tyr cr rep2	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:tyr crispant	GSM7992579	GSM7992579: tyr cr rep2; Danio rerio; RNA Seq	GSM7992579 r1	GSM7992579	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_B_1_S4_L004_R2_001.fastq.gz CR_B_1_S4_L004_R1_001.fastq.gz CR_B_1_S4_L004_I1_001.fastq.gz	fastq fastq fastq	33281519670.0	158483427.0	GSM7992579 r2	0:8 1:101 2:101	A:8932251987;C:6031749264;G:6173441341;T:10874611513;N:1598149	8	101	101		8932251987	6031749264	6173441341	10874611513	1598149	SRX23028810	SRS19990693	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.93392	0.0	0.11469	1.0	0.78928		0.51002	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29481	29481	SRR27352098	SRX23028805	SRS19990688	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1+bhlha15 cr batch C	GSM7992590		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+bhlha15 double crispant\|geo loc name:missing\|collection date:missing	xbp1+bhlha15 cr batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+bhlha15 double crispant	GSM7992590	GSM7992590: xbp1+bhlha15 cr batch C; Danio rerio; RNA Seq	GSM7992590 r1	GSM7992590	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_C_4_S4_L001_I1_001.fastq.gz CR_C_4_S4_L001_I2_001.fastq.gz CR_C_4_S4_L001_R1_001.fastq.gz CR_C_4_S4_L001_R2_001.fastq.gz	fastq fastq fastq fastq	18151441668.0	131532186.0	GSM7992590 r1	0:10 1:10 2:28 3:90	A:3581372515;C:2407649488;G:2925184868;T:2921060975;N:2628894	10	10	28	90	3581372515	2407649488	2925184868	2921060975	2628894	SRX23028805	SRS19990688	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93099		0.14226		0.81562		0.52752		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29482	29482	SRR27352099	SRX23028805	SRS19990688	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1+bhlha15 cr batch C	GSM7992590		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+bhlha15 double crispant\|geo loc name:missing\|collection date:missing	xbp1+bhlha15 cr batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1+bhlha15 double crispant	GSM7992590	GSM7992590: xbp1+bhlha15 cr batch C; Danio rerio; RNA Seq	GSM7992590 r1	GSM7992590	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_C_4_S4_L002_I1_001.fastq.gz CR_C_4_S4_L002_I2_001.fastq.gz CR_C_4_S4_L002_R1_001.fastq.gz CR_C_4_S4_L002_R2_001.fastq.gz	fastq fastq fastq fastq	18006053976.0	130478652.0	GSM7992590 r2	0:10 1:10 2:28 3:90	A:3553087495;C:2385685773;G:2902689895;T:2899003745;N:2611772	10	10	28	90	3553087495	2385685773	2902689895	2899003745	2611772	SRX23028805	SRS19990688	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.92962		0.14303		0.81529		0.50794		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29483	29483	SRR27352100	SRX23028804	SRS19990687	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		bhlha15 cr batch C	GSM7992589		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:bhlha15 crispant\|geo loc name:missing\|collection date:missing	bhlha15 cr batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:bhlha15 crispant	GSM7992589	GSM7992589: bhlha15 cr batch C; Danio rerio; RNA Seq	GSM7992589 r1	GSM7992589	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_C_3_S3_L001_I1_001.fastq.gz CR_C_3_S3_L001_I2_001.fastq.gz CR_C_3_S3_L001_R1_001.fastq.gz CR_C_3_S3_L001_R2_001.fastq.gz	fastq fastq fastq fastq	15376790208.0	111426016.0	GSM7992589 r1	0:10 1:10 2:28 3:90	A:3003756664;C:2055811397;G:2518222694;T:2448321760;N:2228925	10	10	28	90	3003756664	2055811397	2518222694	2448321760	2228925	SRX23028804	SRS19990687	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.9335		0.13891		0.81253		0.52098		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29484	29484	SRR27352101	SRX23028804	SRS19990687	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		bhlha15 cr batch C	GSM7992589		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:bhlha15 crispant\|geo loc name:missing\|collection date:missing	bhlha15 cr batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:bhlha15 crispant	GSM7992589	GSM7992589: bhlha15 cr batch C; Danio rerio; RNA Seq	GSM7992589 r1	GSM7992589	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_C_3_S3_L002_I1_001.fastq.gz CR_C_3_S3_L002_I2_001.fastq.gz CR_C_3_S3_L002_R1_001.fastq.gz CR_C_3_S3_L002_R2_001.fastq.gz	fastq fastq fastq fastq	15177800418.0	109984061.0	GSM7992589 r2	0:10 1:10 2:28 3:90	A:2964523841;C:2027140605;G:2486500514;T:2418183916;N:2216614	10	10	28	90	2964523841	2027140605	2486500514	2418183916	2216614	SRX23028804	SRS19990687	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93069		0.1385		0.8141		0.51224		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29485	29485	SRR27352102	SRX23028803	SRS19990686	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1 cr batch C	GSM7992588		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1 crispant\|geo loc name:missing\|collection date:missing	xbp1 cr batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1 crispant	GSM7992588	GSM7992588: xbp1 cr batch C; Danio rerio; RNA Seq	GSM7992588 r1	GSM7992588	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_C_2_S2_L001_I1_001.fastq.gz CR_C_2_S2_L001_I2_001.fastq.gz CR_C_2_S2_L001_R1_001.fastq.gz CR_C_2_S2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	14244255534.0	103219243.0	GSM7992588 r1	0:10 1:10 2:28 3:90	A:2704750556;C:1968610534;G:2196961227;T:2417349390;N:2060163	10	10	28	90	2704750556	1968610534	2196961227	2417349390	2060163	SRX23028803	SRS19990686	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93364		0.15006		0.78457		0.51247		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29486	29486	SRR27352103	SRX23028803	SRS19990686	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		xbp1 cr batch C	GSM7992588		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1 crispant\|geo loc name:missing\|collection date:missing	xbp1 cr batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:xbp1 crispant	GSM7992588	GSM7992588: xbp1 cr batch C; Danio rerio; RNA Seq	GSM7992588 r1	GSM7992588	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_C_2_S2_L002_I1_001.fastq.gz CR_C_2_S2_L002_I2_001.fastq.gz CR_C_2_S2_L002_R1_001.fastq.gz CR_C_2_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	14098644696.0	102164092.0	GSM7992588 r2	0:10 1:10 2:28 3:90	A:2678755799;C:1946411930;G:2173683067;T:2393852569;N:2064915	10	10	28	90	2678755799	1946411930	2173683067	2393852569	2064915	SRX23028803	SRS19990686	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93345		0.15045		0.78317		0.51621		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29487	29487	SRR27352104	SRX23028802	SRS19990685	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		tyr cr batch C	GSM7992587		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:tyr crispant\|geo loc name:missing\|collection date:missing	tyr cr batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:tyr crispant	GSM7992587	GSM7992587: tyr cr batch C; Danio rerio; RNA Seq	GSM7992587 r1	GSM7992587	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_C_1_S1_L001_R2_001.fastq.gz CR_C_1_S1_L001_R1_001.fastq.gz CR_C_1_S1_L001_I2_001.fastq.gz CR_C_1_S1_L001_I1_001.fastq.gz	fastq fastq fastq fastq	14574404526.0	105611627.0	GSM7992587 r1	0:10 1:10 2:28 3:90	A:2755180826;C:2030934006;G:2268556040;T:2448277539;N:2098019	10	10	28	90	2755180826	2030934006	2268556040	2448277539	2098019	SRX23028802	SRS19990685	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93746		0.15294		0.78486		0.50983		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29488	29488	SRR27352105	SRX23028802	SRS19990685	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		tyr cr batch C	GSM7992587		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:tyr crispant\|geo loc name:missing\|collection date:missing	tyr cr batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:tyr crispant	GSM7992587	GSM7992587: tyr cr batch C; Danio rerio; RNA Seq	GSM7992587 r1	GSM7992587	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_C_1_S1_L002_R2_001.fastq.gz CR_C_1_S1_L002_R1_001.fastq.gz CR_C_1_S1_L002_I2_001.fastq.gz CR_C_1_S1_L002_I1_001.fastq.gz	fastq fastq fastq fastq	14492621310.0	105018995.0	GSM7992587 r2	0:10 1:10 2:28 3:90	A:2741227780;C:2017621877;G:2255130511;T:2435618707;N:2110675	10	10	28	90	2741227780	2017621877	2255130511	2435618707	2110675	SRX23028802	SRS19990685	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93465		0.15149		0.78423		0.52278		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29489	29489	SRR27352106	SRX23028801	SRS19990684	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		atf6+creb3l2+creb3l1 cr	GSM7992578		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant\|geo loc name:missing\|collection date:missing	atf6+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant	GSM7992578	GSM7992578: atf6+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992578 r1	GSM7992578	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_A_8_S32_NOVA3_L001_R2_001.fastq.gz CR_A_8_S32_NOVA3_L001_R1_001.fastq.gz CR_A_8_S32_NOVA3_L001_I1_001.fastq.gz	fastq fastq fastq	1336831751.0	10596395.0	GSM7992578 r1	0:8 1:27.58 2:90.58	A:276155194;C:196755548;G:220643710;T:266282667;N:21935	8	27	90		276155194	196755548	220643710	266282667	21935	SRX23028801	SRS19990684	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93986		0.13023		0.78271		0.49788		91		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29490	29490	SRR27352107	SRX23028801	SRS19990684	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		atf6+creb3l2+creb3l1 cr	GSM7992578		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant\|geo loc name:missing\|collection date:missing	atf6+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant	GSM7992578	GSM7992578: atf6+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992578 r1	GSM7992578	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_A_8_S41_NOVA2_L004_R2_001.fastq.gz CR_A_8_S41_NOVA2_L004_R1_001.fastq.gz CR_A_8_S41_NOVA2_L004_I1_001.fastq.gz	fastq fastq fastq	2244467793.0	17790329.0	GSM7992578 r10	0:8 1:27.58 2:90.59	A:465537689;C:328333906;G:368450917;T:449134468;N:109866	8	27	90		465537689	328333906	368450917	449134468	109866	SRX23028801	SRS19990684	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.9386		0.12988		0.78299		0.48827		91		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29491	29491	SRR27352108	SRX23028801	SRS19990684	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		atf6+creb3l2+creb3l1 cr	GSM7992578		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant\|geo loc name:missing\|collection date:missing	atf6+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant	GSM7992578	GSM7992578: atf6+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992578 r1	GSM7992578	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_A_8_S32_NOVA3_L002_R2_001.fastq.gz CR_A_8_S32_NOVA3_L002_R1_001.fastq.gz CR_A_8_S32_NOVA3_L002_I1_001.fastq.gz	fastq fastq fastq	1335518273.0	10586100.0	GSM7992578 r2	0:8 1:27.57 2:90.58	A:275746202;C:196798646;G:220492715;T:265857008;N:24283	8	27	90		275746202	196798646	220492715	265857008	24283	SRX23028801	SRS19990684	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.9399		0.12887		0.78263		0.50377		89		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29492	29492	SRR27352109	SRX23028801	SRS19990684	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		atf6+creb3l2+creb3l1 cr	GSM7992578		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant\|geo loc name:missing\|collection date:missing	atf6+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant	GSM7992578	GSM7992578: atf6+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992578 r1	GSM7992578	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_A_8_S41_NOVA1_L001_R2_001.fastq.gz CR_A_8_S41_NOVA1_L001_R1_001.fastq.gz CR_A_8_S41_NOVA1_L001_I1_001.fastq.gz	fastq fastq fastq	2979909555.0	23619894.0	GSM7992578 r3	0:8 1:27.58 2:90.58	A:617982744;C:437951840;G:491335568;T:592187571;N:144494	8	27	90		617982744	437951840	491335568	592187571	144494	SRX23028801	SRS19990684	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.9391		0.13086		0.7848		0.50718		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29493	29493	SRR27352110	SRX23028801	SRS19990684	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		atf6+creb3l2+creb3l1 cr	GSM7992578		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant\|geo loc name:missing\|collection date:missing	atf6+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant	GSM7992578	GSM7992578: atf6+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992578 r1	GSM7992578	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_A_8_S41_NOVA1_L002_I1_001.fastq.gz CR_A_8_S41_NOVA1_L002_R1_001.fastq.gz CR_A_8_S41_NOVA1_L002_R2_001.fastq.gz	fastq fastq fastq	3028541832.0	24005329.0	GSM7992578 r4	0:8 1:27.58 2:90.58	A:627626056;C:445411634;G:499743100;T:601587771;N:150767	8	27	90		627626056	445411634	499743100	601587771	150767	SRX23028801	SRS19990684	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.94017		0.12987		0.78366		0.503		89		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29494	29494	SRR27352111	SRX23028801	SRS19990684	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		atf6+creb3l2+creb3l1 cr	GSM7992578		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant\|geo loc name:missing\|collection date:missing	atf6+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant	GSM7992578	GSM7992578: atf6+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992578 r1	GSM7992578	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_A_8_S41_NOVA1_L003_I1_001.fastq.gz CR_A_8_S41_NOVA1_L003_R1_001.fastq.gz CR_A_8_S41_NOVA1_L003_R2_001.fastq.gz	fastq fastq fastq	3035841236.0	24063247.0	GSM7992578 r5	0:8 1:27.58 2:90.58	A:629214519;C:446682769;G:500587257;T:603128429;N:148705	8	27	90		629214519	446682769	500587257	603128429	148705	SRX23028801	SRS19990684	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.94021		0.1306		0.78638		0.49115		91		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29495	29495	SRR27352112	SRX23028801	SRS19990684	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		atf6+creb3l2+creb3l1 cr	GSM7992578		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant\|geo loc name:missing\|collection date:missing	atf6+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant	GSM7992578	GSM7992578: atf6+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992578 r1	GSM7992578	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_A_8_S41_NOVA1_L004_I1_001.fastq.gz CR_A_8_S41_NOVA1_L004_R1_001.fastq.gz CR_A_8_S41_NOVA1_L004_R2_001.fastq.gz	fastq fastq fastq	3052927338.0	24198696.0	GSM7992578 r6	0:8 1:27.58 2:90.58	A:632566746;C:449198284;G:503586649;T:606529377;N:149565	8	27	90		632566746	449198284	503586649	606529377	149565	SRX23028801	SRS19990684	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.94002		0.13095		0.78464		0.49467		91		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	Whole Organism	All anatomical structures
29496	29496	SRR27352113	SRX23028801	SRS19990684	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963		atf6+creb3l2+creb3l1 cr	GSM7992578		source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant\|geo loc name:missing\|collection date:missing	atf6+creb3l2+creb3l1 cr	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:12 hpf\|genotype:atf6+creb3l2 double crispant generated in creb3l1 mutant	GSM7992578	GSM7992578: atf6+creb3l2+creb3l1 cr; Danio rerio; RNA Seq	GSM7992578 r1	GSM7992578	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147		loader:fastq load.py	CR_A_8_S41_NOVA2_L001_R2_001.fastq.gz CR_A_8_S41_NOVA2_L001_R1_001.fastq.gz CR_A_8_S41_NOVA2_L001_I1_001.fastq.gz	fastq fastq fastq	2239550045.0	17751401.0	GSM7992578 r7	0:8 1:27.58 2:90.59	A:464744296;C:327480570;G:367637462;T:448076512;N:104151	8	27	90		464744296	327480570	367637462	448076512	104151	SRX23028801	SRS19990684	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93934		0.12988		0.78253		0.49633		91		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Segmentation	Embryo	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");;