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80 rows where devstage_curation = "Segmentation" and experiment.library_selection = "Oligo-dT"

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tissue_curation 2

technology 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_selection 1

  • Oligo-dT · 80 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Segmentation · 80 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor 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 tech_variant 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
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
26499 26499 SRR26031755 SRX21749012 SRS18856550 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.         RNAseq hand2FACS rtf1MO 3   strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 07 14|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal                 RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos M3 MO3 NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     RNAseq_hand2FACS_rtf1MO_3.fastq fastq 793876754.0 15197870.0 RNAseq hand2FACS rtf1MO 3.fastq 0:52.24 A:208793415;C:174763420;G:174630814;T:235479388;N:209717 52       208793415 174763420 174630814 235479388 209717 SRX21749012 SRS18856550 SRA1709841 University of California, Los Angeles|Molecular, Cell, and Developmental Biology University of California, Los Angeles 1 0.88868   0.1097   0.77644   0.51136   53   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26500 26500 SRR26031756 SRX21749011 SRS18856545 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.         RNAseq hand2FACS rtf1MO 2   strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 07 07|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal                 RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos M2 MO2 NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     RNAseq_hand2FACS_rtf1MO_2.fastq fastq 864787205.0 16568310.0 RNAseq hand2FACS rtf1MO 2.fastq 0:52.20 A:227648729;C:189720880;G:190025417;T:257026454;N:365725 52       227648729 189720880 190025417 257026454 365725 SRX21749011 SRS18856545 SRA1709841 University of California, Los Angeles|Molecular, Cell, and Developmental Biology University of California, Los Angeles 1 0.87433   0.10781   0.77366   0.50792   53   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26501 26501 SRR26031757 SRX21749010 SRS18856549 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.         RNAseq hand2FACS rtf1MO 1   strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 03 04|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal                 RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos M1 MO1 NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     RNAseq_hand2FACS_rtf1MO_1.fastq fastq 821983134.0 15737564.0 RNAseq hand2FACS rtf1MO 1.fastq 0:52.23 A:216610704;C:179969953;G:180145537;T:245093230;N:163710 52       216610704 179969953 180145537 245093230 163710 SRX21749010 SRS18856549 SRA1709841 University of California, Los Angeles|Molecular, Cell, and Developmental Biology University of California, Los Angeles 1 0.88099   0.09837   0.78007   0.50262   53   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26502 26502 SRR26031758 SRX21749009 SRS18856546 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.         RNAseq hand2FACS control 3   strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 02 26|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal                 RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos C3 CTL3 NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     RNAseq_hand2FACS_control_3.fastq fastq 880285441.0 16931477.0 RNAseq hand2FACS control 3.fastq 0:51.99 A:233959122;C:192477087;G:190893530;T:262700285;N:255417 51       233959122 192477087 190893530 262700285 255417 SRX21749009 SRS18856546 SRA1709841 University of California, Los Angeles|Molecular, Cell, and Developmental Biology University of California, Los Angeles 1 0.90285   0.10232   0.76982   0.50837   53   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26503 26503 SRR26031759 SRX21749008 SRS18856548 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.         RNAseq hand2FACS control 2   strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2019 12 19|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal                 RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos C2 CTL2 NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     RNAseq_hand2FACS_control_2.fastq fastq 317458963.0 6417814.0 RNAseq hand2FACS control 2.fastq 0:49.47 A:83925064;C:70621123;G:68872886;T:93923129;N:116761 49       83925064 70621123 68872886 93923129 116761 SRX21749008 SRS18856548 SRA1709841 University of California, Los Angeles|Molecular, Cell, and Developmental Biology University of California, Los Angeles 1 0.85587   0.08493   0.75558   0.51678   50   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26504 26504 SRR26031760 SRX21749007 SRS18856543 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.         RNAseq hand2FACS control 1   strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2019 11 29|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal                 RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos C1 CTL1 NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     RNAseq_hand2FACS_control_1.fastq fastq 448273888.0 9055865.0 RNAseq hand2FACS control 1.fastq 0:49.50 A:119317727;C:99863109;G:96352533;T:132659621;N:80898 49       119317727 99863109 96352533 132659621 80898 SRX21749007 SRS18856543 SRA1709841 University of California, Los Angeles|Molecular, Cell, and Developmental Biology University of California, Los Angeles 1 0.88622   0.09573   0.76086   0.42689   49   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
48722 48722 SRR7789576 SRX4644427 SRS3742497 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 12hpf 2 S5   strain:5D|isolate:68|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 12hpf 2 S5 DMSO 12hpf 2 S5 DMSO 12hpf 2 S5 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     DMSO-12hpf-2_S5_L001_R1_001.fastq.gz fastq 203893981.0 2707574.0 DMSO 12hpf 2 S5 L001 R1 001.fastq.gz 0:75.31 1:0 A:63697786;C:37045141;G:48851781;T:54253873;N:45400 75 0     63697786 37045141 48851781 54253873 45400 SRX4644427 SRS3742497 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.84612   0.21104   0.82075   0.65547   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48723 48723 SRR7789577 SRX4644426 SRS3742496 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 12hpf 1 S1   strain:5D|isolate:67|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 12hpf 1 S1 DMSO 12hpf 1 S1 DMSO 12hpf 1 S1 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     DMSO-12hpf-1_S1_L001_R1_001.fastq.gz fastq 162487810.0 2155953.0 DMSO 12hpf 1 S1 L001 R1 001.fastq.gz 0:75.37 1:0 A:48421887;C:28912597;G:39023644;T:46091677;N:38005 75 0     48421887 28912597 39023644 46091677 38005 SRX4644426 SRS3742496 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.86718   0.17634   0.80706   0.61473   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48724 48724 SRR7789578 SRX4644425 SRS3742495 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DorsoM 12hpf 1 S4   strain:5D|isolate:70|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DorsoM 12hpf 1 S4 DorsoM 12hpf 1 S4 DorsoM 12hpf 1 S4 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     DorsoM-12hpf-1_S4_L001_R1_001.fastq.gz fastq 198651476.0 2638218.0 DorsoM 12hpf 1 S4 L001 R1 001.fastq.gz 0:75.30 1:0 A:60654540;C:36256137;G:48390984;T:53304526;N:45289 75 0     60654540 36256137 48390984 53304526 45289 SRX4644425 SRS3742495 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.83311   0.20053   0.81742   0.60244   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48725 48725 SRR7789579 SRX4644424 SRS3742494 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 12hpf 3 S9   strain:5D|isolate:69|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 12hpf 3 S9 DMSO 12hpf 3 S9 DMSO 12hpf 3 S9 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     DMSO-12hpf-3_S9_L001_R1_001.fastq.gz fastq 297000569.0 3943503.0 DMSO 12hpf 3 S9 L001 R1 001.fastq.gz 0:75.31 1:0 A:93888848;C:52256870;G:67977413;T:82810567;N:66871 75 0     93888848 52256870 67977413 82810567 66871 SRX4644424 SRS3742494 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.85467   0.16577   0.81921   0.6695   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48742 48742 SRR7789596 SRX4644407 SRS3742477 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 156uM 12hpf 1 S2   strain:5D|isolate:73|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 156uM 12hpf 1 S2 TDCIPP 156uM 12hpf 1 S2 TDCIPP 156uM 12hpf 1 S2 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-156uM-12hpf-1_S2_L001_R1_001.fastq.gz fastq 146402685.0 1947438.0 TDCIPP 156uM 12hpf 1 S2 L001 R1 001.fastq.gz                       SRX4644407 SRS3742477 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.65874   0.21238   0.82499   0.44507   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48743 48743 SRR7789597 SRX4644406 SRS3742476 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 156uM 12hpf 2 S6   strain:5D|isolate:74|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 156uM 12hpf 2 S6 TDCIPP 156uM 12hpf 2 S6 TDCIPP 156uM 12hpf 2 S6 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-156uM-12hpf-2_S6_L001_R1_001.fastq.gz fastq 177331004.0 2351198.0 TDCIPP 156uM 12hpf 2 S6 L001 R1 001.fastq.gz 0:75.42 1:0 A:51423657;C:31931003;G:43401496;T:50543110;N:31738 75 0     51423657 31931003 43401496 50543110 31738 SRX4644406 SRS3742476 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.90186   0.18971   0.81215   0.64841   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48744 48744 SRR7789598 SRX4644405 SRS3742475 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DorsoM 12hpf 2 S8   strain:5D|isolate:71|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DorsoM 12hpf 2 S8 DorsoM 12hpf 2 S8 DorsoM 12hpf 2 S8 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     DorsoM-12hpf-2_S8_L001_R1_001.fastq.gz fastq 178023938.0 2362247.0 DorsoM 12hpf 2 S8 L001 R1 001.fastq.gz 0:75.36 1:0 A:54391613;C:31350560;G:41850960;T:50398760;N:32045 75 0     54391613 31350560 41850960 50398760 32045 SRX4644405 SRS3742475 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.86864   0.18173   0.81404   0.6653   72   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48745 48745 SRR7789599 SRX4644404 SRS3742474 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DorsoM 12hpf 3 S12   strain:5D|isolate:72|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DorsoM 12hpf 3 S12 DorsoM 12hpf 3 S12 DorsoM 12hpf 3 S12 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     DorsoM-12hpf-3_S12_L001_R1_001.fastq.gz fastq 201333296.0 2676085.0 DorsoM 12hpf 3 S12 L001 R1 001.fastq.gz 0:75.23 1:0 A:66417840;C:33980802;G:47312604;T:53574703;N:47347 75 0     66417840 33980802 47312604 53574703 47347 SRX4644404 SRS3742474 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.79868   0.18094   0.82229   0.6408   72   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48746 48746 SRR7789600 SRX4644403 SRS3742473 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 312uM 12hpf 2 S7   strain:5D|isolate:77|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 312uM 12hpf 2 S7 TDCIPP 312uM 12hpf 2 S7 TDCIPP 312uM 12hpf 2 S7 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-312uM-12hpf-2_S7_L001_R1_001.fastq.gz fastq 178115275.0 2365002.0 TDCIPP 312uM 12hpf 2 S7 L001 R1 001.fastq.gz 0:75.31 1:0 A:56273985;C:30179061;G:41734280;T:49890330;N:37619 75 0     56273985 30179061 41734280 49890330 37619 SRX4644403 SRS3742473 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.84673   0.14158   0.80819   0.65468   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48747 48747 SRR7789601 SRX4644402 SRS3742472 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 312uM 12hpf 3 S11   strain:5D|isolate:78|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 312uM 12hpf 3 S11 TDCIPP 312uM 12hpf 3 S11 TDCIPP 312uM 12hpf 3 S11 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-312uM-12hpf-3_S11_L001_R1_001.fastq.gz fastq 207620778.0 2756303.0 TDCIPP 312uM 12hpf 3 S11 L001 R1 001.fastq.gz 0:75.33 1:0 A:64831167;C:35550977;G:47406669;T:59788673;N:43292 75 0     64831167 35550977 47406669 59788673 43292 SRX4644402 SRS3742472 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.85126   0.15334   0.81682   0.64899   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48748 48748 SRR7789602 SRX4644401 SRS3742471 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 156uM 12hpf 3 S10   strain:5D|isolate:75|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 156uM 12hpf 3 S10 TDCIPP 156uM 12hpf 3 S10 TDCIPP 156uM 12hpf 3 S10 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-156uM-12hpf-3_S10_L001_R1_001.fastq.gz fastq 222002176.0 2945967.0 TDCIPP 156uM 12hpf 3 S10 L001 R1 001.fastq.gz 0:75.36 1:0 A:67404952;C:39276717;G:51982070;T:63295632;N:42805 75 0     67404952 39276717 51982070 63295632 42805 SRX4644401 SRS3742471 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.87086   0.19188   0.81615   0.66924   72   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48749 48749 SRR7789603 SRX4644400 SRS3742470 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 312uM 12hpf 1 S3   strain:5D|isolate:76|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 312uM 12hpf 1 S3 TDCIPP 312uM 12hpf 1 S3 TDCIPP 312uM 12hpf 1 S3 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-312uM-12hpf-1_S3_L001_R1_001.fastq.gz fastq 203425925.0 2701005.0 TDCIPP 312uM 12hpf 1 S3 L001 R1 001.fastq.gz 0:75.31 1:0 A:63029639;C:36056635;G:49899459;T:54398131;N:42061 75 0     63029639 36056635 49899459 54398131 42061 SRX4644400 SRS3742470 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.83498   0.18597   0.81473   0.62049   72   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
53836 53836 SRR10393501 SRX7093892 SRS5606542 SRP228416 PRJNA563973 High Content Screening in Zebrafish Identifies Perfluorooctanesulfonamide PFOSA as a Potent Developmental Toxicant PRJNA563973 Other The objective of this study was to rely on mRNA sequencing to quantify whole transcriptome responses to perfluorooctanesulfonamide PFOSA exposure within the first 24 h of zebrafish development.         PFOSA 14hpf 2 S11   strain:5D|isolate:10|dev stage:14 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 PFOSA 14hpf 2 S11 PFOSA 14hpf 2 S11 PFOSA 14hpf 2 S11 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP228416     PFOSA-14hpf-2_S11_L001_R1_001.fastq.gz fastq 199280173.0 2654129.0 PFOSA 14hpf 2 S11 L001 R1 001.fastq.gz 0:75.08 1:0 A:69633326;C:40325635;G:55611717;T:33071326;N:638169 75 0     69633326 40325635 55611717 33071326 638169 SRX7093892 SRS5606542 SRA989836 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.59602   0.24178   0.8802   0.57219   75   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2019-11-05 Segmentation Embryo Embryo Imprecise All anatomical structures
53837 53837 SRR10393502 SRX7093891 SRS5606541 SRP228416 PRJNA563973 High Content Screening in Zebrafish Identifies Perfluorooctanesulfonamide PFOSA as a Potent Developmental Toxicant PRJNA563973 Other The objective of this study was to rely on mRNA sequencing to quantify whole transcriptome responses to perfluorooctanesulfonamide PFOSA exposure within the first 24 h of zebrafish development.         PFOSA 14hpf 1 S10   strain:5D|isolate:9|dev stage:14 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 PFOSA 14hpf 1 S10 PFOSA 14hpf 1 S10 PFOSA 14hpf 1 S10 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP228416     PFOSA-14hpf-1_S10_L001_R1_001.fastq.gz fastq 227687219.0 3043008.0 PFOSA 14hpf 1 S10 L001 R1 001.fastq.gz 0:74.82 1:0 A:77107329;C:47499687;G:61809986;T:39670141;N:1600076 74 0     77107329 47499687 61809986 39670141 1600076 SRX7093891 SRS5606541 SRA989836 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.62016   0.24853   0.86801   0.42508   75   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2019-11-05 Segmentation Embryo Embryo Imprecise All anatomical structures
53842 53842 SRR10393507 SRX7093886 SRS5606536 SRP228416 PRJNA563973 High Content Screening in Zebrafish Identifies Perfluorooctanesulfonamide PFOSA as a Potent Developmental Toxicant PRJNA563973 Other The objective of this study was to rely on mRNA sequencing to quantify whole transcriptome responses to perfluorooctanesulfonamide PFOSA exposure within the first 24 h of zebrafish development.         DMSO 14hpf 4 S13   strain:5D|isolate:4|dev stage:14 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 14hpf 4 S13 DMSO 14hpf 4 S13 DMSO 14hpf 4 S13 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP228416     DMSO-14hpf-4_S13_L001_R1_001.fastq.gz fastq 192268250.0 2553116.0 DMSO 14hpf 4 S13 L001 R1 001.fastq.gz 0:75.31 1:0 A:64412753;C:40190901;G:48579795;T:38885554;N:199247 75 0     64412753 40190901 48579795 38885554 199247 SRX7093886 SRS5606536 SRA989836 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.74204   0.24082   0.83932   0.61852   75   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2019-11-05 Segmentation Embryo Embryo Imprecise All anatomical structures
53843 53843 SRR10393508 SRX7093885 SRS5606535 SRP228416 PRJNA563973 High Content Screening in Zebrafish Identifies Perfluorooctanesulfonamide PFOSA as a Potent Developmental Toxicant PRJNA563973 Other The objective of this study was to rely on mRNA sequencing to quantify whole transcriptome responses to perfluorooctanesulfonamide PFOSA exposure within the first 24 h of zebrafish development.         DMSO 14hpf 3 S9   strain:5D|isolate:3|dev stage:14 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 14hpf 3 S9 DMSO 14hpf 3 S9 DMSO 14hpf 3 S9 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP228416     DMSO-14hpf-3_S9_L001_R1_001.fastq.gz fastq 215390173.0 2865220.0 DMSO 14hpf 3 S9 L001 R1 001.fastq.gz 0:75.17 1:0 A:80603037;C:40812476;G:57293446;T:36197170;N:484044 75 0     80603037 40812476 57293446 36197170 484044 SRX7093885 SRS5606535 SRA989836 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.53337   0.1878   0.87458   0.58419   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2019-11-05 Segmentation Embryo Embryo Imprecise All anatomical structures
53848 53848 SRR10393513 SRX7093880 SRS5606530 SRP228416 PRJNA563973 High Content Screening in Zebrafish Identifies Perfluorooctanesulfonamide PFOSA as a Potent Developmental Toxicant PRJNA563973 Other The objective of this study was to rely on mRNA sequencing to quantify whole transcriptome responses to perfluorooctanesulfonamide PFOSA exposure within the first 24 h of zebrafish development.         PFOSA 14hpf 4 S14   strain:5D|isolate:12|dev stage:14 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 PFOSA 14hpf 4 S14 PFOSA 14hpf 4 S14 PFOSA 14hpf 4 S14 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP228416     PFOSA-14hpf-4_S14_L001_R1_001.fastq.gz fastq 200250875.0 2660819.0 PFOSA 14hpf 4 S14 L001 R1 001.fastq.gz 0:75.26 1:0 A:71094635;C:39966633;G:49516955;T:39370603;N:302049 75 0     71094635 39966633 49516955 39370603 302049 SRX7093880 SRS5606530 SRA989836 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.68291   0.21892   0.85263   0.66356   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2019-11-05 Segmentation Embryo Embryo Imprecise All anatomical structures
53849 53849 SRR10393514 SRX7093879 SRS5606529 SRP228416 PRJNA563973 High Content Screening in Zebrafish Identifies Perfluorooctanesulfonamide PFOSA as a Potent Developmental Toxicant PRJNA563973 Other The objective of this study was to rely on mRNA sequencing to quantify whole transcriptome responses to perfluorooctanesulfonamide PFOSA exposure within the first 24 h of zebrafish development.         PFOSA 14hpf 3 S12   strain:5D|isolate:11|dev stage:14 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 PFOSA 14hpf 3 S12 PFOSA 14hpf 3 S12 PFOSA 14hpf 3 S12 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP228416     PFOSA-14hpf-3_S12_L001_R1_001.fastq.gz fastq 205880924.0 2738339.0 PFOSA 14hpf 3 S12 L001 R1 001.fastq.gz 0:75.18 1:0 A:73593616;C:40882580;G:54885999;T:35974173;N:544556 75 0     73593616 40882580 54885999 35974173 544556 SRX7093879 SRS5606529 SRA989836 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.60517   0.22568   0.86989   0.6311   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2019-11-05 Segmentation Embryo Embryo Imprecise All anatomical structures
53850 53850 SRR10393515 SRX7093878 SRS5606528 SRP228416 PRJNA563973 High Content Screening in Zebrafish Identifies Perfluorooctanesulfonamide PFOSA as a Potent Developmental Toxicant PRJNA563973 Other The objective of this study was to rely on mRNA sequencing to quantify whole transcriptome responses to perfluorooctanesulfonamide PFOSA exposure within the first 24 h of zebrafish development.         DMSO 14hpf 2 S8   strain:5D|isolate:2|dev stage:14 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 14hpf 2 S8 DMSO 14hpf 2 S8 DMSO 14hpf 2 S8 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP228416     DMSO-14hpf-2_S8_L001_R1_001.fastq.gz fastq 205823576.0 2741804.0 DMSO 14hpf 2 S8 L001 R1 001.fastq.gz 0:75.07 1:0 A:76605742;C:38535627;G:53129399;T:36836758;N:716050 75 0     76605742 38535627 53129399 36836758 716050 SRX7093878 SRS5606528 SRA989836 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.59432   0.17094   0.86005   0.62198   75   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2019-11-05 Segmentation Embryo Embryo Imprecise All anatomical structures
53851 53851 SRR10393516 SRX7093877 SRS5606527 SRP228416 PRJNA563973 High Content Screening in Zebrafish Identifies Perfluorooctanesulfonamide PFOSA as a Potent Developmental Toxicant PRJNA563973 Other The objective of this study was to rely on mRNA sequencing to quantify whole transcriptome responses to perfluorooctanesulfonamide PFOSA exposure within the first 24 h of zebrafish development.         DMSO 14hpf 1 S7   strain:5D|isolate:1|dev stage:14 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 14hpf 1 S7 DMSO 14hpf 1 S7 DMSO 14hpf 1 S7 QuantSeq three prime mRNA Seq Library Prep Kit FWD     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiniSeq   SRP228416     DMSO-14hpf-1_S7_L001_R1_001.fastq.gz fastq 17828000.0 236767.0 DMSO 14hpf 1 S7 L001 R1 001.fastq.gz 0:75.30 1:0 A:6272160;C:3525377;G:4410500;T:3595551;N:24412 75 0     6272160 3525377 4410500 3595551 24412 SRX7093877 SRS5606527 SRA989836 University of California, Riverside|Environmental Sciences University of California, Riverside 1 0.66234   0.19959   0.84153   0.60524   76   B   usable mapping rate illumina miseq 3prime poly_a lexogen bulk unknown unknown   United States 2019-11-05 Segmentation Embryo Embryo Imprecise All anatomical structures
60657 60657 SRR15046102 SRX11356738 SRS9403587 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.     scRNAseq scRNAseq Satb2 MUT 14som scRNAseq Satb2 MUT 14som   strain:Satb2 Mutant|age:14 somite|dev stage:14 somite|sex:not applicable|tissue:whole embryo|replicate:replicate = Biological replicate1|BioSampleModel:Model organism or animal                 Satb2 mutants single cell RNAseq Satb2 MUT 14ss scRNAseq Satb2 MUT 14ss scRNAseq according 10X three primemRNA seq V3.2 protocol     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA NextSeq 550   SRP278034   loader:fastq load.py     23142978710.0 177123922.0 scRNAseq Satb2 MUT 14som I1.fastq.gz 0:8 1:30 2:92.66 A:4753575949;C:3375880000;G:3751151628;T:4500225651;N:31436446 8 30 92   4753575949 3375880000 3751151628 4500225651 31436446 SRX11356738 SRS9403587 SRA1254741 IISER-PUNE|biology IISER-PUNE 1 0.80351   0.14479   0.79695   0.55274   101   B   usable mapping rate illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   India 2021-07-13 Segmentation Embryo Whole Organism All anatomical structures
60658 60658 SRR15046103 SRX11356737 SRS9403586 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.     scRNAseq scRNAseq WT 14som scRNAseq WT 14som   strain:Wild type sibling|age:14 somite|dev stage:14 somite|sex:not applicable|tissue:whole embryo|replicate:replicate = Biological replicate1|BioSampleModel:Model organism or animal                 Satb2 siblings single cell RNAseq WT sibs 14ss scRNAseq WT sibs 14ss scRNAseq according 10X three primemRNA seq V3.2 protocol     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA NextSeq 550   SRP278034   loader:fastq load.py|options: mixedDeflines maxErrorCount=0     27847103625.0 200338875.0 scRNAseq WT 14som I1.fastq.gz 0:8 1:30 2:101 A:5948912529;C:4138132473;G:4588280753;T:5527087357;N:31813263 8 30 101   5948912529 4138132473 4588280753 5527087357 31813263 SRX11356737 SRS9403586 SRA1254741 IISER-PUNE|biology IISER-PUNE 1 0.92298   0.15133   0.78906   0.54933   101   B   usable mapping rate illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   India 2021-07-13 Segmentation Embryo Whole Organism All anatomical structures
60659 60659 SRR12474618 SRX8968764 SRS7224501 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.       Quantseq 14som WT BR2 Quantseq 14som WT Rep2   strain:TU|isolate:wild type|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 hpf|dev stage:14 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=14som WT Rep2|BioSampleModel:Model organism or animal                 Quantseq 14som WT BR2 Quantseq 14som WT Rep2 Quantseq 14som WT Rep2 3 mRNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP278034     Quantseq_14som_WT_Rep2.fastq.gz fastq 903044063.0 12000242.0 Quantseq 14som WT Rep2.fastq.gz 0:75.25 1:0 A:263352708;C:185236415;G:232384431;T:221833596;N:236913 75 0     263352708 185236415 232384431 221833596 236913 SRX8968764 SRS7224501 SRA1114017 IISER-PUNE|biology IISER-PUNE 1 0.42684   0.07198   0.85003   0.59691   76   B   usable mapping rate illumina nextseq 3prime poly_a unknown bulk unknown unknown   India 2020-08-19 Segmentation Embryo Whole Organism All anatomical structures
60660 60660 SRR12474619 SRX8968763 SRS7224500 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.       Quantseq 14som WT BR1 Quantseq 14som WT Rep1   strain:TU|isolate:wild type|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 hpf|dev stage:14 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=14som WT Rep1|BioSampleModel:Model organism or animal                 Quantseq 14som WT BR1 Quantseq 14som WT Rep1 Quantseq 14som WT Rep1 3 mRNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP278034     Quantseq_14som_WT_Rep1.fastq.gz fastq 882525364.0 11721403.0 Quantseq 14som WT Rep1.fastq.gz 0:75.29 1:0 A:259807886;C:175863634;G:225108328;T:221642061;N:103455 75 0     259807886 175863634 225108328 221642061 103455 SRX8968763 SRS7224500 SRA1114017 IISER-PUNE|biology IISER-PUNE 1 0.53254   0.08405   0.8341   0.60885   75   B   usable mapping rate illumina nextseq 3prime poly_a unknown bulk unknown unknown   India 2020-08-19 Segmentation Embryo Whole Organism All anatomical structures
60661 60661 SRR12474620 SRX8968762 SRS7224499 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.       Quantseq 6som SATB2 MUT BR2 Quantseq 6som SATB2 MUT Rep2   strain:TU|isolate:Satb2 mutant|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:6 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=6som SATB2 MUT Rep2|BioSampleModel:Model organism or animal                 Quantseq 6som SATB2 MUT BR2 Quantseq 6som SATB2 MUT Rep2 Quantseq 6som SATB2 MUT Rep2 3 mRNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP278034     Quantseq_6som_SATB2_MUT_Rep2.fastq.gz fastq 881413896.0 11727371.0 Quantseq 6som SATB2 MUT Rep2.fastq.gz 0:75.16 1:0 A:247870923;C:186063682;G:234789338;T:212038718;N:651235 75 0     247870923 186063682 234789338 212038718 651235 SRX8968762 SRS7224499 SRA1114017 IISER-PUNE|biology IISER-PUNE 1 0.49309   0.11767   0.85109   0.64403   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   India 2020-08-19 Segmentation Embryo Whole Organism All anatomical structures
60667 60667 SRR12474626 SRX8968756 SRS7224493 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.       Quantseq 6som SATB2 MUT BR1 Quantseq 6som SATB2 MUT Rep1   strain:TU|isolate:Satb2 mutant|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:6 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=6som SATB2 MUT Rep1|BioSampleModel:Model organism or animal                 Quantseq 6som SATB2 MUT BR1 Quantseq 6som SATB2 MUT Rep1 Quantseq 6som SATB2 MUT Rep1 3 mRNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP278034     Quantseq_6som_SATB2_MUT_Rep1.fastq.gz fastq 800824696.0 10638604.0 Quantseq 6som SATB2 MUT Rep1.fastq.gz 0:75.28 1:0 A:227510912;C:166510969;G:206664296;T:199873805;N:264714 75 0     227510912 166510969 206664296 199873805 264714 SRX8968756 SRS7224493 SRA1114017 IISER-PUNE|biology IISER-PUNE 1 0.40209   0.09672   0.86736   0.41916   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   India 2020-08-19 Segmentation Embryo Whole Organism All anatomical structures
60673 60673 SRR12474637 SRX8968745 SRS7224482 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.       Quantseq 6som WT BR2 Quantseq 6som WT Rep2   strain:TU|isolate:wild type|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:6 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=6som WT Rep2|BioSampleModel:Model organism or animal                 Quantseq 6som WT BR2 Quantseq 6som WT Rep2 Quantseq 6som WT Rep2 3 mRNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP278034     Quantseq_6som_WT_Rep2.fastq.gz fastq 725351601.0 9625088.0 Quantseq 6som WT Rep2.fastq.gz 0:75.36 1:0 A:207416580;C:148728596;G:183133392;T:185967953;N:105080 75 0     207416580 148728596 183133392 185967953 105080 SRX8968745 SRS7224482 SRA1114017 IISER-PUNE|biology IISER-PUNE 1 0.40444   0.07771   0.87018   0.63186   75   B   usable mapping rate illumina nextseq 3prime poly_a unknown bulk unknown unknown   India 2020-08-19 Segmentation Embryo Whole Organism All anatomical structures
60674 60674 SRR12474648 SRX8968734 SRS7224471 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.       Quantseq 6som WT BR1 Quantseq 6som WT Rep1   strain:TU|isolate:wild type|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:6 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=6som WT Rep1|BioSampleModel:Model organism or animal                 Quantseq 6som WT BR1 Quantseq 6som WT Rep1 Quantseq 6som WT Rep1 3 mRNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP278034     Quantseq_6som_WT_Rep1.fastq.gz fastq 708766045.0 9408553.0 Quantseq 6som WT Rep1.fastq.gz 0:75.33 1:0 A:206111164;C:145117557;G:179409280;T:178028436;N:99608 75 0     206111164 145117557 179409280 178028436 99608 SRX8968734 SRS7224471 SRA1114017 IISER-PUNE|biology IISER-PUNE 1 0.31065   0.05507   0.8831   0.66855   76   B   usable mapping rate illumina nextseq 3prime poly_a unknown bulk unknown unknown   India 2020-08-19 Segmentation Embryo Whole Organism All anatomical structures
60677 60677 SRR12474679 SRX8968703 SRS7224440 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.       Quantseq 14som SATB2 MUT BR2 Quantseq 14som SATB2 MUT Rep2   strain:TU|isolate:Satb2 mutant|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 hpf|dev stage:14 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=14som SATB2 MUT Rep2|BioSampleModel:Model organism or animal                 Quantseq 14som SATB2 MUT BR2 Quantseq 14som SATB2 MUT Rep2 Quantseq 14som SATB2 MUT Rep2 3 mRNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP278034     Quantseq_14som_SATB2_MUT_Rep2.fastq.gz fastq 807655188.0 10715264.0 Quantseq 14som SATB2 MUT Rep2.fastq.gz 0:75.37 1:0 A:236716025;C:162286136;G:202282454;T:206318628;N:51945 75 0     236716025 162286136 202282454 206318628 51945 SRX8968703 SRS7224440 SRA1114017 IISER-PUNE|biology IISER-PUNE 1 0.49529   0.07146   0.85683   0.65015   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   India 2020-08-19 Segmentation Embryo Whole Organism All anatomical structures
60678 60678 SRR12474680 SRX8968702 SRS7224439 SRP278034 PRJNA657343 Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development PRJNA657343 Other Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.       Quantseq 14som SATB2 MUT BR1 Quantseq 14som SATB2 MUT Rep1   strain:TU|isolate:Satb2 mutant|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 hpf|dev stage:14 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=14som SATB2 MUT Rep1|BioSampleModel:Model organism or animal                 Quantseq 14som SATB2 MUT BR1 Quantseq 14som SATB2 MUT Rep1 Quantseq 14som SATB2 MUT Rep1 3 mRNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP278034     Quantseq_14som_SATB2_MUT_Rep1.fastq.gz fastq 714114566.0 9480391.0 Quantseq 14som SATB2 MUT Rep1.fastq.gz 0:75.33 1:0 A:214876091;C:138572440;G:176756219;T:183862261;N:47555 75 0     214876091 138572440 176756219 183862261 47555 SRX8968702 SRS7224439 SRA1114017 IISER-PUNE|biology IISER-PUNE 1 0.53567   0.06484   0.84618   0.64745   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   India 2020-08-19 Segmentation Embryo Whole Organism All anatomical structures
70098 70098 SRR19543887 SRX15595980 SRS13296994 SRP378531 PRJNA846086 Danio rerio strain:AB Raw sequence reads PRJNA846086 Whole Genome Sequencing Nomal RNA seq of zebrafish         BPA3   strain:AB|age:11hpf|dev stage:5 9 somites|sex:pooled male and female|tissue:embryo|treatment:30μM BPA|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: embryo BPA3 BPA3 Normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378531     BPA3_1.fq.gz BPA3_2.fq.gz fastq fastq 6778769700.0 22595899.0 BPA3 1.fq.gz 0:150 1:150 A:1795637973;C:1607358128;G:1599499184;T:1776043517;N:230898 150 150     1795637973 1607358128 1599499184 1776043517 230898 SRX15595980 SRS13296994 SRA1431736 University of Macau|Faculty of Health and Sciences University of Macau 2 0.95484 0.95375 0.06941 0.06927 0.72484 0.72516 0.46488 0.46852 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-06 Segmentation Embryo Embryo Imprecise All anatomical structures
70099 70099 SRR19543888 SRX15595979 SRS13296993 SRP378531 PRJNA846086 Danio rerio strain:AB Raw sequence reads PRJNA846086 Whole Genome Sequencing Nomal RNA seq of zebrafish         BPA2   strain:AB|age:11hpf|dev stage:5 9 somites|sex:pooled male and female|tissue:embryo|treatment:30μM BPA|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: embryo BPA2 BPA2 Normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378531     BPA2_1.fq.gz BPA2_2.fq.gz fastq fastq 6696197700.0 22320659.0 BPA2 1.fq.gz 0:150 1:150 A:1787447154;C:1576391068;G:1564345742;T:1767778281;N:235455 150 150     1787447154 1576391068 1564345742 1767778281 235455 SRX15595979 SRS13296993 SRA1431736 University of Macau|Faculty of Health and Sciences University of Macau 2 0.95565 0.95375 0.07562 0.0752 0.72145 0.722 0.4767 0.47823 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-06 Segmentation Embryo Embryo Imprecise All anatomical structures
70100 70100 SRR19543889 SRX15595978 SRS13296992 SRP378531 PRJNA846086 Danio rerio strain:AB Raw sequence reads PRJNA846086 Whole Genome Sequencing Nomal RNA seq of zebrafish         BPA1   strain:AB|age:11hpf|dev stage:5 9 somites|sex:pooled male and female|tissue:embryo|treatment:30μM BPA|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: embryo BPA1 BPA1 Normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378531     BPA1_1.fq.gz BPA1_2.fq.gz fastq fastq 6104923800.0 20349746.0 BPA1 1.fq.gz 0:150 1:150 A:1619470868;C:1446280371;G:1438807953;T:1600108341;N:256267 150 150     1619470868 1446280371 1438807953 1600108341 256267 SRX15595978 SRS13296992 SRA1431736 University of Macau|Faculty of Health and Sciences University of Macau 2 0.95425 0.95232 0.06962 0.06897 0.72567 0.72614 0.46747 0.47231 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-06 Segmentation Embryo Embryo Imprecise All anatomical structures
70101 70101 SRR19543890 SRX15595977 SRS13296991 SRP378531 PRJNA846086 Danio rerio strain:AB Raw sequence reads PRJNA846086 Whole Genome Sequencing Nomal RNA seq of zebrafish         Con3   strain:AB|age:11hpf|dev stage:5 9 somites|sex:pooled male and female|tissue:embryo|treatment:control|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: embryo Con3 Con3 Normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378531     Con3_1.fq.gz Con3_2.fq.gz fastq fastq 6858985200.0 22863284.0 Con3 1.fq.gz 0:150 1:150 A:1824825391;C:1620714911;G:1610367588;T:1802785647;N:291663 150 150     1824825391 1620714911 1610367588 1802785647 291663 SRX15595977 SRS13296991 SRA1431736 University of Macau|Faculty of Health and Sciences University of Macau 2 0.95302 0.95122 0.0756 0.07505 0.72356 0.72397 0.46846 0.46956 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-06 Segmentation Embryo Embryo Imprecise All anatomical structures
70102 70102 SRR19543891 SRX15595976 SRS13296990 SRP378531 PRJNA846086 Danio rerio strain:AB Raw sequence reads PRJNA846086 Whole Genome Sequencing Nomal RNA seq of zebrafish         Con2   strain:AB|age:11hpf|dev stage:5 9 somites|sex:pooled male and female|tissue:embryo|treatment:control|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: embryo Con2 Con2 Normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378531     Con2_1.fq.gz Con2_2.fq.gz fastq fastq 7062888600.0 23542962.0 Con2 1.fq.gz 0:150 1:150 A:1878260174;C:1667874410;G:1660396460;T:1856098232;N:259324 150 150     1878260174 1667874410 1660396460 1856098232 259324 SRX15595976 SRS13296990 SRA1431736 University of Macau|Faculty of Health and Sciences University of Macau 2 0.95201 0.9512 0.07122 0.07084 0.72736 0.72817 0.46496 0.46625 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-06 Segmentation Embryo Embryo Imprecise All anatomical structures
70103 70103 SRR19543892 SRX15595975 SRS13296989 SRP378531 PRJNA846086 Danio rerio strain:AB Raw sequence reads PRJNA846086 Whole Genome Sequencing Nomal RNA seq of zebrafish         Con1   strain:AB|age:11hpf|dev stage:5 9 somites|sex:pooled male and female|tissue:embryo|treatment:control|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: embryo Con1 Con1 Normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378531     Con1_1.fq.gz Con1_2.fq.gz fastq fastq 6795739800.0 22652466.0 Con1 1.fq.gz 0:150 1:150 A:1820854131;C:1593155735;G:1582883837;T:1798595392;N:250705 150 150     1820854131 1593155735 1582883837 1798595392 250705 SRX15595975 SRS13296989 SRA1431736 University of Macau|Faculty of Health and Sciences University of Macau 2 0.95063 0.94915 0.07901 0.07831 0.72305 0.72336 0.4782 0.48038 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-06 Segmentation Embryo Embryo Imprecise All anatomical structures

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