{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Segmentation\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[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.  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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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. 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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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. 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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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. 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Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. 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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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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 3\u02b9 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired 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 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u0e2a\u0e19 GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 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", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, null, "RNAseq hand2FACS rtf1MO 3", null, "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", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "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, null, null, null, 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, null, 0.1097, null, 0.77644, null, 0.51136, null, 53, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, null, "RNAseq hand2FACS rtf1MO 2", null, "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", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "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, null, null, null, 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, null, 0.10781, null, 0.77366, null, 0.50792, null, 53, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, null, "RNAseq hand2FACS rtf1MO 1", null, "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", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "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, null, null, null, 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, null, 0.09837, null, 0.78007, null, 0.50262, null, 53, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, null, "RNAseq hand2FACS control 3", null, "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", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "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, null, null, null, 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, null, 0.10232, null, 0.76982, null, 0.50837, null, 53, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, null, "RNAseq hand2FACS control 2", null, "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", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "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, null, null, null, 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, null, 0.08493, null, 0.75558, null, 0.51678, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, null, "RNAseq hand2FACS control 1", null, "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", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "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, null, null, null, 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, null, 0.09573, null, 0.76086, null, 0.42689, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28625, "SRR26502015", "SRX22205863", "SRS19261273", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "U 2S C", "GSM7863853", null, "tissue:Zebrafish embryo explants|condition:uninjected U controls|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "U 2S C", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:uninjected U controls|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863853", "GSM7863853: U 2S C; Danio rerio; RNA Seq", "GSM7863853 r1", "GSM7863853", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "U_2S_C_1.fq.gz U_2S_C_2.fq.gz", "fastq fastq", 7566478800.0, 25221596.0, "GSM7863853 r1", "0:150 1:150", "A:2026550144;C:1766328106;G:1769959517;T:2003575689;N:65344", 150, 150, null, null, 2026550144, 1766328106, 1769959517, 2003575689, 65344, "SRX22205863", "SRS19261273", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.96377, 0.96417, 0.09722, 0.09709, 0.74535, 0.74592, 0.4741, 0.4748, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28626, "SRR26502016", "SRX22205862", "SRS19261269", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "U 2S B", "GSM7863852", null, "tissue:Zebrafish embryo explants|condition:uninjected U controls|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "U 2S B", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:uninjected U controls|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863852", "GSM7863852: U 2S B; Danio rerio; RNA Seq", "GSM7863852 r1", "GSM7863852", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "U_2S_B_1.fq.gz U_2S_B_2.fq.gz", "fastq fastq", 7891113000.0, 26303710.0, "GSM7863852 r1", "0:150 1:150", "A:2124525120;C:1831314650;G:1831884848;T:2103320675;N:67707", 150, 150, null, null, 2124525120, 1831314650, 1831884848, 2103320675, 67707, "SRX22205862", "SRS19261269", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.963, 0.96272, 0.10371, 0.10304, 0.74416, 0.74509, 0.47491, 0.4783, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28627, "SRR26502017", "SRX22205861", "SRS19261270", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "U 2S A", "GSM7863851", null, "tissue:Zebrafish embryo explants|condition:uninjected U controls|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "U 2S A", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:uninjected U controls|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863851", "GSM7863851: U 2S A; Danio rerio; RNA Seq", "GSM7863851 r1", "GSM7863851", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "U_2S_A_1.fq.gz U_2S_A_2.fq.gz", "fastq fastq", 7382820300.0, 24609401.0, "GSM7863851 r1", "0:150 1:150", "A:1982413721;C:1717733326;G:1720628836;T:1961981713;N:62704", 150, 150, null, null, 1982413721, 1717733326, 1720628836, 1961981713, 62704, "SRX22205861", "SRS19261270", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.96215, 0.96285, 0.10366, 0.10356, 0.74263, 0.74458, 0.46685, 0.46662, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28658, "SRR26502048", "SRX22205830", "SRS19261238", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "T 2S C", "GSM7863832", null, "tissue:Zebrafish embryo explants|condition:constitutively active Nodal receptor CA acvr1b* T|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "T 2S C", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:constitutively active Nodal receptor CA acvr1b* T|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863832", "GSM7863832: T 2S C; Danio rerio; RNA Seq", "GSM7863832 r1", "GSM7863832", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "T_2S_C_1.fq.gz T_2S_C_2.fq.gz", "fastq fastq", 6433508100.0, 21445027.0, "GSM7863832 r1", "0:150 1:150", "A:1727786029;C:1494465422;G:1498183536;T:1713018480;N:54633", 150, 150, null, null, 1727786029, 1494465422, 1498183536, 1713018480, 54633, "SRX22205830", "SRS19261238", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.9661, 0.96638, 0.10089, 0.1, 0.74647, 0.74683, 0.47525, 0.47285, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28659, "SRR26502049", "SRX22205829", "SRS19261236", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "T 2S B", "GSM7863831", null, "tissue:Zebrafish embryo explants|condition:constitutively active Nodal receptor CA acvr1b* T|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "T 2S B", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:constitutively active Nodal receptor CA acvr1b* T|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863831", "GSM7863831: T 2S B; Danio rerio; RNA Seq", "GSM7863831 r1", "GSM7863831", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "T_2S_B_1.fq.gz T_2S_B_2.fq.gz", "fastq fastq", 8306095800.0, 27686986.0, "GSM7863831 r1", "0:150 1:150", "A:2233558794;C:1929667711;G:1941489485;T:2201309961;N:69849", 150, 150, null, null, 2233558794, 1929667711, 1941489485, 2201309961, 69849, "SRX22205829", "SRS19261236", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.96232, 0.9621, 0.10279, 0.10181, 0.73338, 0.73472, 0.4597, 0.43955, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28660, "SRR26502050", "SRX22205828", "SRS19261237", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "T 2S A", "GSM7863830", null, "tissue:Zebrafish embryo explants|condition:constitutively active Nodal receptor CA acvr1b* T|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "T 2S A", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:constitutively active Nodal receptor CA acvr1b* T|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863830", "GSM7863830: T 2S A; Danio rerio; RNA Seq", "GSM7863830 r1", "GSM7863830", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "T_2S_A_1.fq.gz T_2S_A_2.fq.gz", "fastq fastq", 6689336100.0, 22297787.0, "GSM7863830 r1", "0:150 1:150", "A:1800205357;C:1554352939;G:1554832665;T:1779888062;N:57077", 150, 150, null, null, 1800205357, 1554352939, 1554832665, 1779888062, 57077, "SRX22205828", "SRS19261237", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.96497, 0.96515, 0.09779, 0.09719, 0.7469, 0.74783, 0.47049, 0.4664, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28679, "SRR26502069", "SRX22205809", "SRS19261217", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "N 2S C", "GSM7863811", null, "tissue:Zebrafish embryo explants|condition:Nodal ligand ndr2 N|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "N 2S C", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:Nodal ligand ndr2 N|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863811", "GSM7863811: N 2S C; Danio rerio; RNA Seq", "GSM7863811 r1", "GSM7863811", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "N_2S_C_1.fq.gz N_2S_C_2.fq.gz", "fastq fastq", 8377883400.0, 27926278.0, "GSM7863811 r1", "0:150 1:150", "A:2254561592;C:1945354110;G:1946954800;T:2230940768;N:72130", 150, 150, null, null, 2254561592, 1945354110, 1946954800, 2230940768, 72130, "SRX22205809", "SRS19261217", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.96358, 0.96422, 0.10583, 0.10604, 0.74032, 0.74213, 0.45254, 0.45311, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28680, "SRR26502070", "SRX22205808", "SRS19261216", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "N 2S B", "GSM7863810", null, "tissue:Zebrafish embryo explants|condition:Nodal ligand ndr2 N|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "N 2S B", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:Nodal ligand ndr2 N|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863810", "GSM7863810: N 2S B; Danio rerio; RNA Seq", "GSM7863810 r1", "GSM7863810", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "N_2S_B_1.fq.gz N_2S_B_2.fq.gz", "fastq fastq", 6049027800.0, 20163426.0, "GSM7863810 r1", "0:150 1:150", "A:1642862477;C:1393234786;G:1391276933;T:1621546261;N:107343", 150, 150, null, null, 1642862477, 1393234786, 1391276933, 1621546261, 107343, "SRX22205808", "SRS19261216", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.96105, 0.9602, 0.10217, 0.10102, 0.75081, 0.75043, 0.46937, 0.4667, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28681, "SRR26502071", "SRX22205807", "SRS19261215", "SRP468205", "PRJNA1031674", "Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants", "GSE246158", "Transcriptome Analysis", "We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N  constitutively active Nodal receptor CA acvr1b* T  and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR  zfs:0000015 30  50% epiboly 50  shield SH  75% epiboly 75  90% epiboly 90  and 2 somite 2S corresponding to 4  4.7  5.3  6  8  9  and 11 hpf  respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N  CA acvr1b*T  and uninjected U explants with 3 biological replicates A C per condition per stage SR   2S.", null, "pubmed:39651654", null, "N 2S A", "GSM7863809", null, "tissue:Zebrafish embryo explants|condition:Nodal ligand ndr2 N|developmental stage:2 somite 2S|stage index:7|geo loc name:missing|collection date:missing", "N 2S A", "Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Zebrafish embryo explants", "Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA  respectively", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", "Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection", "condition:Nodal ligand ndr2 N|developmental stage:2 somite 2S|approx time hpf index:7", "GSM7863809", "GSM7863809: N 2S A; Danio rerio; RNA Seq", "GSM7863809 r1", "GSM7863809", "1", "Total RNA was isolated using Trizol reagent  then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468205", null, "loader:fastq load.py", "N_2S_A_1.fq.gz N_2S_A_2.fq.gz", "fastq fastq", 8840694300.0, 29468981.0, "GSM7863809 r1", "0:150 1:150", "A:2361587582;C:2065699253;G:2075417505;T:2337833496;N:156464", 150, 150, null, null, 2361587582, 2065699253, 2075417505, 2337833496, 156464, "SRX22205807", "SRS19261215", "SRA1738892", "Baylor College of Medicine", "Baylor College of Medicine", 2, 0.96054, 0.95851, 0.10583, 0.10529, 0.74452, 0.74531, 0.44973, 0.45305, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-24", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30014, "SRR28164888", "SRX23795140", "SRS20618184", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, "10x Genomics multiplexing  CMO", "scRNA seq  wild type and hamp /   12 hpf  CMO", "Zebrafish embryo scRNA seq  wild type and hamp /   12 hpf  CMO", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:12 hpf  CMO|dev stage:12 hpf  CMO|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq  wild type and hamp /   12 hpf  CMO", "C 1", "C 1", "10x Genomics multiplexing  CMO", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "12h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 12h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz", "fastq fastq", 23801259900.0, 79337533.0, "12h Multiplexing Capture S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:5110000752;C:5818733743;G:7758205963;T:5113684708;N:634734", 150, 150, null, null, 5110000752, 5818733743, 7758205963, 5113684708, 634734, "SRX23795140", "SRS20618184", "SRA1813495", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, null, null, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-02-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30017, "SRR28164891", "SRX23795137", "SRS20618181", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, "10x Genomics multiplexing  GEX", "scRNA seq  wild type and hamp /   12 hpf  GEX", "Zebrafish embryo scRNA seq  wild type and hamp /   12 hpf  GEX", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:12 hpf  GEX|dev stage:12 hpf  GEX|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq  wild type and hamp /   12 hpf  GEX", "G 1", "G 1", "10x Genomics multiplexing  GEX", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "12h_Gene_Expression_S1_L001_R2_001.fastq.gz 12h_Gene_Expression_S1_L001_R1_001.fastq.gz", "fastq fastq", 204426398700.0, 681421329.0, "12h Gene Expression S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:61302872939;C:35072603645;G:37153666376;T:70891933893;N:5321847", 150, 150, null, null, 61302872939, 35072603645, 37153666376, 70891933893, 5321847, "SRX23795137", "SRS20618181", "SRA1813495", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.00085, 0.9058, 0.0, 0.12081, 0.99991, 0.80231, 0.5, 0.52456, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-02-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30028, "SRR27732024", "SRX23397624", "SRS20258465", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "wild type 12 hpf embryo", "zebrafish embryo 12hpf replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 12hpf embryo", "W 9", "W 9", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT12h-3_1.fq.gz WT12h-3_2.fq.gz", "fastq fastq", 6455561100.0, 21518537.0, "WT12h 3 1.fq.gz", "0:150 1:150", "A:1703515693;C:1511743995;G:1560331864;T:1679864521;N:105027", 150, 150, null, null, 1703515693, 1511743995, 1560331864, 1679864521, 105027, "SRX23397624", "SRS20258465", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94111, 0.94086, 0.06759, 0.06714, 0.74383, 0.74479, 0.46264, 0.46309, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30029, "SRR27732025", "SRX23397623", "SRS20258464", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "wild type 12 hpf embryo", "zebrafish embryo 12hpf replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 12hpf embryo", "W 8", "W 8", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT12h-2_1.fq.gz WT12h-2_2.fq.gz", "fastq fastq", 6161839200.0, 20539464.0, "WT12h 2 1.fq.gz", "0:150 1:150", "A:1628002733;C:1440787634;G:1486546983;T:1606403484;N:98366", 150, 150, null, null, 1628002733, 1440787634, 1486546983, 1606403484, 98366, "SRX23397623", "SRS20258464", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94064, 0.93857, 0.06897, 0.06866, 0.7457, 0.74621, 0.46575, 0.46211, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30030, "SRR27732026", "SRX23397622", "SRS20258463", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "wild type 12 hpf embryo", "zebrafish embryo 12hpf replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 12hpf embryo", "W 7", "W 7", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT12h-1_2.fq.gz WT12h-1_1.fq.gz", "fastq fastq", 6395259000.0, 21317530.0, "WT12h 1 1.fq.gz", "0:150 1:150", "A:1700786034;C:1487669685;G:1530455534;T:1676243983;N:103764", 150, 150, null, null, 1700786034, 1487669685, 1530455534, 1676243983, 103764, "SRX23397622", "SRS20258463", "SRA1791946", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.94192, 0.9393, 0.07278, 0.0714, 0.74225, 0.74414, 0.46258, 0.46623, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-26", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30043, "SRR27730706", "SRX23396352", "SRS20257266", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "hamp /  12 hpf embryo", "zebrafish embryo hamp /  12hpf replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 12hpf embryo", "W 30", "W 30", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp12h-3_1.fq.gz hamp12h-3_2.fq.gz", "fastq fastq", 6380262000.0, 21267540.0, "hamp12h 3 1.fq.gz", "0:150 1:150", "A:1686482981;C:1496556670;G:1525661866;T:1671347887;N:212596", 150, 150, null, null, 1686482981, 1496556670, 1525661866, 1671347887, 212596, "SRX23396352", "SRS20257266", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.93955, 0.93782, 0.07021, 0.07017, 0.72541, 0.72691, 0.4754, 0.47596, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30044, "SRR27730707", "SRX23396351", "SRS20257265", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "hamp /  12 hpf embryo", "zebrafish embryo hamp /  12hpf replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 12hpf embryo", "W 29", "W 29", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp12h-2_1.fq.gz hamp12h-2_2.fq.gz", "fastq fastq", 6738373500.0, 22461245.0, "hamp12h 2 1.fq.gz", "0:150 1:150", "A:1793407846;C:1570428903;G:1600911780;T:1773421988;N:202983", 150, 150, null, null, 1793407846, 1570428903, 1600911780, 1773421988, 202983, "SRX23396351", "SRS20257265", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.93629, 0.93637, 0.07013, 0.07043, 0.72764, 0.72912, 0.47138, 0.47279, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30045, "SRR27730708", "SRX23396350", "SRS20257264", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "hamp /  12 hpf embryo", "zebrafish embryo hamp /  12hpf replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 12hpf embryo", "W 28", "W 28", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "hamp12h-1_1.fq.gz hamp12h-1_2.fq.gz", "fastq fastq", 6882364200.0, 22941214.0, "hamp12h 1 1.fq.gz", "0:150 1:150", "A:1816338301;C:1617411981;G:1650700092;T:1797708715;N:205111", 150, 150, null, null, 1816338301, 1617411981, 1650700092, 1797708715, 205111, "SRX23396350", "SRS20257264", "SRA1791861", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.93465, 0.93675, 0.06811, 0.06816, 0.72863, 0.72922, 0.47838, 0.47563, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31557, "SRR28471021", "SRX24074012", "SRS20864401", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 13", "GSM8171995", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 13", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171995", "GSM8171995: S16 slice 13; Danio rerio; RNA Seq", "GSM8171995 r1", "GSM8171995", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_13-R1.fq.gz S16_2_13-R2.fq.gz", "fastq fastq", 7021136766.0, 24220886.0, "GSM8171995 r1", "0:143.40 1:146.48", "A:1932409729;C:1613003140;G:1510879854;T:1964782006;N:62037", 143, 146, null, null, 1932409729, 1613003140, 1510879854, 1964782006, 62037, "SRX24074012", "SRS20864401", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31558, "SRR28471022", "SRX24074011", "SRS20864400", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 12", "GSM8171993", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 12", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171993", "GSM8171993: S16 slice 12; Danio rerio; RNA Seq", "GSM8171993 r1", "GSM8171993", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_12-R1.fq.gz S16_2_12-R2.fq.gz", "fastq fastq", 6989496704.0, 24013496.0, "GSM8171993 r1", "0:144.73 1:146.34", "A:1973063613;C:1539634004;G:1502105630;T:1974633280;N:60177", 144, 146, null, null, 1973063613, 1539634004, 1502105630, 1974633280, 60177, "SRX24074011", "SRS20864400", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31559, "SRR28471023", "SRX24074010", "SRS20864399", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 11", "GSM8171992", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 11", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171992", "GSM8171992: S16 slice 11; Danio rerio; RNA Seq", "GSM8171992 r1", "GSM8171992", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_11-R1.fq.gz S16_2_11-R2.fq.gz", "fastq fastq", 6658580843.0, 22968779.0, "GSM8171992 r1", "0:143.28 1:146.62", "A:1850547171;C:1505778383;G:1450300777;T:1851895401;N:59111", 143, 146, null, null, 1850547171, 1505778383, 1450300777, 1851895401, 59111, "SRX24074010", "SRS20864399", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31560, "SRR28471024", "SRX24074009", "SRS20864398", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 10", "GSM8171991", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 10", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171991", "GSM8171991: S16 slice 10; Danio rerio; RNA Seq", "GSM8171991 r1", "GSM8171991", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_10-R1.fq.gz S16_2_10-R2.fq.gz", "fastq fastq", 6764254234.0, 23283773.0, "GSM8171991 r1", "0:143.52 1:146.99", "A:1876570759;C:1531892471;G:1478929048;T:1876804139;N:57817", 143, 146, null, null, 1876570759, 1531892471, 1478929048, 1876804139, 57817, "SRX24074009", "SRS20864398", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31561, "SRR28471025", "SRX24074008", "SRS20864397", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 9", "GSM8171990", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 9", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171990", "GSM8171990: S16 slice 9; Danio rerio; RNA Seq", "GSM8171990 r1", "GSM8171990", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_09-R1.fq.gz S16_2_09-R2.fq.gz", "fastq fastq", 6953469676.0, 23939332.0, "GSM8171990 r1", "0:143.01 1:147.45", "A:1887466615;C:1613826863;G:1550286679;T:1901843452;N:46067", 143, 147, null, null, 1887466615, 1613826863, 1550286679, 1901843452, 46067, "SRX24074008", "SRS20864397", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31562, "SRR28471026", "SRX24074007", "SRS20864396", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 8", "GSM8171989", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 8", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171989", "GSM8171989: S16 slice 8; Danio rerio; RNA Seq", "GSM8171989 r1", "GSM8171989", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_08-R1.fq.gz S16_2_08-R2.fq.gz", "fastq fastq", 6932164944.0, 23736001.0, "GSM8171989 r1", "0:144.93 1:147.12", "A:1878823532;C:1592513147;G:1541045989;T:1919723182;N:59094", 144, 147, null, null, 1878823532, 1592513147, 1541045989, 1919723182, 59094, "SRX24074007", "SRS20864396", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31563, "SRR28471027", "SRX24074006", "SRS20864395", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 7", "GSM8171987", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 7", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171987", "GSM8171987: S16 slice 7; Danio rerio; RNA Seq", "GSM8171987 r1", "GSM8171987", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_07-R1.fq.gz S16_2_07-R2.fq.gz", "fastq fastq", 7175124342.0, 24613098.0, "GSM8171987 r1", "0:144.89 1:146.63", "A:1955179901;C:1642901455;G:1556429416;T:2020550025;N:63545", 144, 146, null, null, 1955179901, 1642901455, 1556429416, 2020550025, 63545, "SRX24074006", "SRS20864395", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31564, "SRR28471028", "SRX24074005", "SRS20864394", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 6", "GSM8171986", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 6", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171986", "GSM8171986: S16 slice 6; Danio rerio; RNA Seq", "GSM8171986 r1", "GSM8171986", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_06-R1.fq.gz S16_2_06-R2.fq.gz", "fastq fastq", 7015063214.0, 24014594.0, "GSM8171986 r1", "0:145.26 1:146.86", "A:1907017747;C:1603933957;G:1551829473;T:1952222046;N:59991", 145, 146, null, null, 1907017747, 1603933957, 1551829473, 1952222046, 59991, "SRX24074005", "SRS20864394", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31565, "SRR28471029", "SRX24074004", "SRS20864393", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 5", "GSM8171985", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 5", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171985", "GSM8171985: S16 slice 5; Danio rerio; RNA Seq", "GSM8171985 r1", "GSM8171985", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_05-R1.fq.gz S16_2_05-R2.fq.gz", "fastq fastq", 6919538718.0, 23740085.0, "GSM8171985 r1", "0:144.96 1:146.51", "A:1882346373;C:1593041314;G:1504597309;T:1939492468;N:61254", 144, 146, null, null, 1882346373, 1593041314, 1504597309, 1939492468, 61254, "SRX24074004", "SRS20864393", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31566, "SRR28471030", "SRX24074003", "SRS20864392", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 4", "GSM8171984", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 4", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171984", "GSM8171984: S16 slice 4; Danio rerio; RNA Seq", "GSM8171984 r1", "GSM8171984", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_04-R1.fq.gz S16_2_04-R2.fq.gz", "fastq fastq", 6868276226.0, 23671591.0, "GSM8171984 r1", "0:144.21 1:145.94", "A:1877392790;C:1565333202;G:1481973920;T:1943515595;N:60719", 144, 145, null, null, 1877392790, 1565333202, 1481973920, 1943515595, 60719, "SRX24074003", "SRS20864392", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31567, "SRR28471031", "SRX24074002", "SRS20864391", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 3", "GSM8171983", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 3", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171983", "GSM8171983: S16 slice 3; Danio rerio; RNA Seq", "GSM8171983 r1", "GSM8171983", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_03-R1.fq.gz S16_2_03-R2.fq.gz", "fastq fastq", 6805653527.0, 23393184.0, "GSM8171983 r1", "0:144.38 1:146.54", "A:1865258599;C:1547577456;G:1497746987;T:1895011008;N:59477", 144, 146, null, null, 1865258599, 1547577456, 1497746987, 1895011008, 59477, "SRX24074002", "SRS20864391", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31568, "SRR28471032", "SRX24074001", "SRS20864390", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 2", "GSM8171981", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 2", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171981", "GSM8171981: S16 slice 2; Danio rerio; RNA Seq", "GSM8171981 r1", "GSM8171981", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_02-R1.fq.gz S16_2_02-R2.fq.gz", "fastq fastq", 7023963229.0, 24162141.0, "GSM8171981 r1", "0:144.12 1:146.58", "A:1918527133;C:1603910134;G:1551695853;T:1949772309;N:57800", 144, 146, null, null, 1918527133, 1603910134, 1551695853, 1949772309, 57800, "SRX24074001", "SRS20864390", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31569, "SRR28471033", "SRX24074000", "SRS20864389", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S16 slice 1", "GSM8171980", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing", "S16 slice 1", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:16 hpf", "GSM8171980", "GSM8171980: S16 slice 1; Danio rerio; RNA Seq", "GSM8171980 r1", "GSM8171980", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S16_2_01-R1.fq.gz S16_2_01-R2.fq.gz", "fastq fastq", 6619993068.0, 22789527.0, "GSM8171980 r1", "0:143.43 1:147.06", "A:1776228931;C:1542516186;G:1481044120;T:1820158687;N:45144", 143, 147, null, null, 1776228931, 1542516186, 1481044120, 1820158687, 45144, "SRX24074000", "SRS20864389", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31570, "SRR28471034", "SRX24073999", "SRS20864388", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 12", "GSM8171979", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 12", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171979", "GSM8171979: S12 slice 12; Danio rerio; RNA Seq", "GSM8171979 r1", "GSM8171979", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_12-R1.fq.gz S12_1_12-R2.fq.gz", "fastq fastq", 6907282671.0, 23557012.0, "GSM8171979 r1", "0:145.54 1:147.68", "A:1862944199;C:1601198280;G:1521830219;T:1921292527;N:17446", 145, 147, null, null, 1862944199, 1601198280, 1521830219, 1921292527, 17446, "SRX24073999", "SRS20864388", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31571, "SRR28471035", "SRX24073998", "SRS20864387", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 11", "GSM8171978", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 11", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171978", "GSM8171978: S12 slice 11; Danio rerio; RNA Seq", "GSM8171978 r1", "GSM8171978", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_11-R1.fq.gz S12_1_11-R2.fq.gz", "fastq fastq", 6831871099.0, 23334246.0, "GSM8171978 r1", "0:145.23 1:147.56", "A:1841130963;C:1590884839;G:1490156717;T:1909681306;N:17274", 145, 147, null, null, 1841130963, 1590884839, 1490156717, 1909681306, 17274, "SRX24073998", "SRS20864387", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31572, "SRR28471036", "SRX24073997", "SRS20864386", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 10", "GSM8171977", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 10", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171977", "GSM8171977: S12 slice 10; Danio rerio; RNA Seq", "GSM8171977 r1", "GSM8171977", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_10-R1.fq.gz S12_1_10-R2.fq.gz", "fastq fastq", 5783041643.0, 19665431.0, "GSM8171977 r1", "0:146.19 1:147.88", "A:1581046379;C:1324978876;G:1248026718;T:1628974699;N:14971", 146, 147, null, null, 1581046379, 1324978876, 1248026718, 1628974699, 14971, "SRX24073997", "SRS20864386", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31573, "SRR28471037", "SRX24073996", "SRS20864385", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 9", "GSM8171976", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 9", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171976", "GSM8171976: S12 slice 9; Danio rerio; RNA Seq", "GSM8171976 r1", "GSM8171976", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_09-R1.fq.gz S12_1_09-R2.fq.gz", "fastq fastq", 7123142895.0, 24299296.0, "GSM8171976 r1", "0:145.49 1:147.66", "A:1925297375;C:1659640314;G:1576196761;T:1961990580;N:17865", 145, 147, null, null, 1925297375, 1659640314, 1576196761, 1961990580, 17865, "SRX24073996", "SRS20864385", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31574, "SRR28471038", "SRX24073995", "SRS20864384", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 8", "GSM8171974", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 8", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171974", "GSM8171974: S12 slice 8; Danio rerio; RNA Seq", "GSM8171974 r1", "GSM8171974", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_08-R1.fq.gz S12_1_08-R2.fq.gz", "fastq fastq", 7144819692.0, 24316501.0, "GSM8171974 r1", "0:145.93 1:147.90", "A:1915884877;C:1672968137;G:1576641332;T:1979307110;N:18236", 145, 147, null, null, 1915884877, 1672968137, 1576641332, 1979307110, 18236, "SRX24073995", "SRS20864384", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31575, "SRR28471039", "SRX24073994", "SRS20864383", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 7", "GSM8171973", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 7", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171973", "GSM8171973: S12 slice 7; Danio rerio; RNA Seq", "GSM8171973 r1", "GSM8171973", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_07-R1.fq.gz S12_1_07-R2.fq.gz", "fastq fastq", 7379485401.0, 25300209.0, "GSM8171973 r1", "0:143.87 1:147.81", "A:1973584695;C:1736374415;G:1654430758;T:2015077010;N:18523", 143, 147, null, null, 1973584695, 1736374415, 1654430758, 2015077010, 18523, "SRX24073994", "SRS20864383", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31576, "SRR28471040", "SRX24073993", "SRS20864382", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 6", "GSM8171972", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 6", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171972", "GSM8171972: S12 slice 6; Danio rerio; RNA Seq", "GSM8171972 r1", "GSM8171972", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_06-R1.fq.gz S12_1_06-R2.fq.gz", "fastq fastq", 6780830499.0, 23111786.0, "GSM8171972 r1", "0:145.59 1:147.80", "A:1809593504;C:1599719267;G:1512122288;T:1859381851;N:13589", 145, 147, null, null, 1809593504, 1599719267, 1512122288, 1859381851, 13589, "SRX24073993", "SRS20864382", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31577, "SRR28471041", "SRX24073992", "SRS20864381", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 5", "GSM8171971", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 5", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171971", "GSM8171971: S12 slice 5; Danio rerio; RNA Seq", "GSM8171971 r1", "GSM8171971", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_05-R1.fq.gz S12_1_05-R2.fq.gz", "fastq fastq", 6959350050.0, 23769190.0, "GSM8171971 r1", "0:145.06 1:147.72", "A:1875092128;C:1615063748;G:1550970555;T:1918160024;N:63595", 145, 147, null, null, 1875092128, 1615063748, 1550970555, 1918160024, 63595, "SRX24073992", "SRS20864381", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31578, "SRR28471042", "SRX24073991", "SRS20864380", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 4", "GSM8171970", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 4", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171970", "GSM8171970: S12 slice 4; Danio rerio; RNA Seq", "GSM8171970 r1", "GSM8171970", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_04-R1.fq.gz S12_1_04-R2.fq.gz", "fastq fastq", 7016331930.0, 23929575.0, "GSM8171970 r1", "0:145.36 1:147.85", "A:1883672645;C:1639902329;G:1566256062;T:1926486960;N:13934", 145, 147, null, null, 1883672645, 1639902329, 1566256062, 1926486960, 13934, "SRX24073991", "SRS20864380", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31579, "SRR28471043", "SRX24073990", "SRS20864379", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 3", "GSM8171968", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 3", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171968", "GSM8171968: S12 slice 3; Danio rerio; RNA Seq", "GSM8171968 r1", "GSM8171968", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_03-R1.fq.gz S12_1_03-R2.fq.gz", "fastq fastq", 7014757897.0, 23928375.0, "GSM8171968 r1", "0:145.38 1:147.78", "A:1893627672;C:1629188725;G:1555319202;T:1936558222;N:64076", 145, 147, null, null, 1893627672, 1629188725, 1555319202, 1936558222, 64076, "SRX24073990", "SRS20864379", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31580, "SRR28471044", "SRX24073989", "SRS20864378", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 2", "GSM8171967", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 2", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171967", "GSM8171967: S12 slice 2; Danio rerio; RNA Seq", "GSM8171967 r1", "GSM8171967", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_02-R1.fq.gz S12_1_02-R2.fq.gz", "fastq fastq", 6840908671.0, 23398529.0, "GSM8171967 r1", "0:144.87 1:147.50", "A:1887167845;C:1555902053;G:1495740904;T:1902033708;N:64161", 144, 147, null, null, 1887167845, 1555902053, 1495740904, 1902033708, 64161, "SRX24073989", "SRS20864378", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31581, "SRR28471045", "SRX24073988", "SRS20864376", "SRP498123", "PRJNA1092581", "Construction of Danio rerio Asymmetrical Maps DreAM", "GSE262578", "Transcriptome Analysis", "Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.", null, null, null, "S12 slice 1", "GSM8171966", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing", "S12 slice 1", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.", "embryonic cells", "Embedded embryos were cryosectioned at a thickness of 20 \u00b5m. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", "Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.", "tissue:embryonic cells|strain:AB|age:12 hpf", "GSM8171966", "GSM8171966: S12 slice 1; Danio rerio; RNA Seq", "GSM8171966 r1", "GSM8171966", "1", "RNA was extracted using PicoPure\u2122 RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq\u2122 Stranded mRNA LT Sample Prep Kit following the standard protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498123", null, "loader:fastq load.py", "S12_1_01-R1.fq.gz S12_1_01-R2.fq.gz", "fastq fastq", 7278647579.0, 24915967.0, "GSM8171966 r1", "0:144.68 1:147.45", "A:1978225177;C:1677337831;G:1598910902;T:2024108056;N:65613", 144, 147, null, null, 1978225177, 1677337831, 1598910902, 2024108056, 65613, "SRX24073988", "SRS20864376", "SRA1834502", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2024-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31876, "SRR28764744", "SRX24330058", "SRS21091016", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 22h", "GSM8222579", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf loc name:missing|collection date:missing", "CEL210312AN WT 22h", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf", "GSM8222579", "GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq", "GSM8222579 r1", "GSM8222579", "1", "Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_22h_S96_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S96_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S96_L003_R2_001.fastq.gz", "fastq fastq fastq", 9045377769.0, 71223447.0, "GSM8222579 r1", "0:8 1:28 2:91", "A:1910521348;C:1357874019;G:1521970464;T:1690926373;N:41473", 8, 28, 91, null, 1910521348, 1357874019, 1521970464, 1690926373, 41473, "SRX24330058", "SRS21091016", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31877, "SRR28764745", "SRX24330058", "SRS21091016", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 22h", "GSM8222579", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf loc name:missing|collection date:missing", "CEL210312AN WT 22h", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf", "GSM8222579", "GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq", "GSM8222579 r1", "GSM8222579", "1", "Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_22h_S97_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S97_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S97_L003_R2_001.fastq.gz", "fastq fastq fastq", 9556753429.0, 75250027.0, "GSM8222579 r2", "0:8 1:28 2:91", "A:2016694527;C:1436202913;G:1608693558;T:1786117733;N:43726", 8, 28, 91, null, 2016694527, 1436202913, 1608693558, 1786117733, 43726, "SRX24330058", "SRS21091016", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31878, "SRR28764746", "SRX24330058", "SRS21091016", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 22h", "GSM8222579", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf loc name:missing|collection date:missing", "CEL210312AN WT 22h", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf", "GSM8222579", "GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq", "GSM8222579 r1", "GSM8222579", "1", "Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_22h_S98_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S98_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S98_L003_R2_001.fastq.gz", "fastq fastq fastq", 6838295188.0, 53844844.0, "GSM8222579 r3", "0:8 1:28 2:91", "A:1443225941;C:1028068269;G:1151922277;T:1276632644;N:31673", 8, 28, 91, null, 1443225941, 1028068269, 1151922277, 1276632644, 31673, "SRX24330058", "SRS21091016", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31879, "SRR28764747", "SRX24330058", "SRS21091016", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 22h", "GSM8222579", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf loc name:missing|collection date:missing", "CEL210312AN WT 22h", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf", "GSM8222579", "GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq", "GSM8222579 r1", "GSM8222579", "1", "Twenty two hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_22h_S99_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S99_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S99_L003_R2_001.fastq.gz", "fastq fastq fastq", 8872634401.0, 69863263.0, "GSM8222579 r4", "0:8 1:28 2:91", "A:1873119195;C:1332238982;G:1493221194;T:1658936897;N:40665", 8, 28, 91, null, 1873119195, 1332238982, 1493221194, 1658936897, 40665, "SRX24330058", "SRS21091016", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31880, "SRR28738013", "SRX24303940", "SRS21066774", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 14h", "GSM8216056", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf loc name:missing|collection date:missing", "CEL210312AN WT 14h", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf", "GSM8216056", "GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq", "GSM8216056 r1", "GSM8216056", "1", "Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_14h_S92_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S92_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S92_L003_R2_001.fastq.gz", "fastq fastq fastq", 5909782440.0, 46533720.0, "GSM8216056 r1", "0:8 1:28 2:91", "A:1195361841;C:933687818;G:1057254177;T:1048237872;N:26812", 8, 28, 91, null, 1195361841, 933687818, 1057254177, 1048237872, 26812, "SRX24303940", "SRS21066774", "SRA1848682", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-18", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31881, "SRR28738014", "SRX24303940", "SRS21066774", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 14h", "GSM8216056", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf loc name:missing|collection date:missing", "CEL210312AN WT 14h", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf", "GSM8216056", "GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq", "GSM8216056 r1", "GSM8216056", "1", "Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_14h_S93_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S93_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S93_L003_R2_001.fastq.gz", "fastq fastq fastq", 6519796333.0, 51336979.0, "GSM8216056 r2", "0:8 1:28 2:91", "A:1320007258;C:1029906863;G:1166350676;T:1155370144;N:30148", 8, 28, 91, null, 1320007258, 1029906863, 1166350676, 1155370144, 30148, "SRX24303940", "SRS21066774", "SRA1848682", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-18", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31882, "SRR28738015", "SRX24303940", "SRS21066774", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 14h", "GSM8216056", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf loc name:missing|collection date:missing", "CEL210312AN WT 14h", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf", "GSM8216056", "GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq", "GSM8216056 r1", "GSM8216056", "1", "Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_14h_S94_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S94_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S94_L003_R2_001.fastq.gz", "fastq fastq fastq", 6288014983.0, 49511929.0, "GSM8216056 r3", "0:8 1:28 2:91", "A:1273032152;C:992961980;G:1124384567;T:1115177910;N:28930", 8, 28, 91, null, 1273032152, 992961980, 1124384567, 1115177910, 28930, "SRX24303940", "SRS21066774", "SRA1848682", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-18", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31883, "SRR28738016", "SRX24303940", "SRS21066774", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 14h", "GSM8216056", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf loc name:missing|collection date:missing", "CEL210312AN WT 14h", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf", "GSM8216056", "GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq", "GSM8216056 r1", "GSM8216056", "1", "Fourteen hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_14h_S95_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S95_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S95_L003_R2_001.fastq.gz", "fastq fastq fastq", 6986621409.0, 55012767.0, "GSM8216056 r4", "0:8 1:28 2:91", "A:1412426673;C:1104618149;G:1250890162;T:1238194657;N:32156", 8, 28, 91, null, 1412426673, 1104618149, 1250890162, 1238194657, 32156, "SRX24303940", "SRS21066774", "SRA1848682", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-18", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35979, "SRR33380663", "SRX28623695", "SRS24895016", "SRP582260", "PRJNA1256738", "Angptl5 restricts primitive hematopoiesis by modulating retinoic acid signaling in zebrafish", "GSE295891", "Other", "Purpose: Characterization of cell types in angptl5?10/?10 zebrafish. Methods: The angptl5?10/?10 embryos were raised in 0.3\u00d7 Danieau Buffer and harvested at 16 hpf. Collected samples were digested with trypsin into single cell suspension for single cell sequencing. Libraries were constructed with  a Chromium Single Cell three primev3 Reagent Kit 10x Genomics according to the manufacturer's protocol for 7350 cell recovery.Sequencing was performed with Illumina Novaseq 6000 according to the manufacturer's instructions Illumina. Results:  Global amplification of myeloid and erythroid progenitors in angptl5?10/?10 embryos. Conclusions: Angptl5 regulated primitive hematopoiesis in zebrafish. Overall design: Collected samples of angptl5?10/?10 embryos at 16 hpf were digested with trypsin into single cell suspension for  scRNA seq.", null, null, null, "A5 /  16 hpf", "GSM8960245", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|cell type:embryonic cells|genotype:angptl5 mutant|treatment:CRISPR/Cas9 knockout|batch:A5 16h|geo loc name:missing|collection date:missing", "A5 /  16 hpf", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar compressed  files include filtered gene bc matrices post running CellRanger pipeline", "embryonic cells", "Collected samples were digested with trypsin into single cell suspension and set to Novogene for single cell sequencing.", "RNA from the barcoded cells was reverse transcribed  reagents from a Chromium Single Cell reagent kit 10X Genomics Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3 10x Genomics  Cat# PN 1000268 according to the manufacturer\u2019s protocol for 7350 cell recovery.", "The angptl5\u039410/\u039410 embryos were raised in 0.3\u00d7 Danieau Buffer and harvested at 16 hpf", "tissue:embryonic cells|strain:AB|cell type:embryonic cells|genotype:angptl5 mutant|treatment:CRISPR/Cas9 knockout|batch:A5 16h", "GSM8960245", "GSM8960245: A5 /  16 hpf; Danio rerio; RNA Seq", "GSM8960245 r1", "GSM8960245", "1", "RNA from the barcoded cells was reverse transcribed  reagents from a Chromium Single Cell reagent kit 10X Genomics Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3 10x Genomics  Cat# PN 1000268 according to the manufacturer's protocol for 7350 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582260", null, null, "A5_16h-zebra_S1_L001_R1_001.fastq.gz A5_16h-zebra_S1_L001_R2_001.fastq.gz", "fastq fastq", 126632686800.0, 422108956.0, "GSM8960245 r1", "0:150 1:150", "A:31741347954;C:28608734203;G:22541136036;T:43733881512;N:7587095", 150, 150, null, null, 31741347954, 28608734203, 22541136036, 43733881512, 7587095, "SRX28623695", "SRS24895016", "SRA2121245", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-04-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36212, "SRR33570992", "SRX28800977", "SRS25038275", "SRP585332", "PRJNA1262902", "BCAS2 promotes primitive hematopoiesis by sequestering \u00df catenin within the nucleus", "GSE297155", "Transcriptome Analysis", "Breast carcinoma amplified sequence 2 BCAS2  a core component of the hPrP19 complex  plays crucial roles in various physiological and pathological processes. However  whether BCAS2 has functions other than being a key RNA splicing regulator within the nucleus remains unknown. Here  we show that BCAS2 is essential for primitive hematopoiesis in zebrafish and mouse embryos. The activation of Wnt/\u00df catenin signal  which is required for hematopoietic progenitor differentiation  is significantly decreased upon depletion of bcas2 in zebrafish embryos and mouse embryonic fibroblasts MEFs. Interestingly  BCAS2 de?ciency has no obvious impact on the splicing efficiency of \u00df catenin pre mRNA  while significantly attenuating \u00df catenin nuclear accumulation. Moreover  we find that BCAS2 directly binds to \u00df catenin via its coiled coil domains  thereby sequestering \u00df catenin within the nucleus. Thus  our results uncover a previously unknown function of BCAS2 in promoting Wnt signaling by enhancing \u00df catenin nuclear retention during primitive hematopoiesis. Overall design: RNA sequencing profiling for wild type and bcas2 +/?14 embryos at 10 ss.", null, null, null, "b14", "GSM8984757", null, "source name:embryo|tissue:embryo|genotype:heterozygous|geo loc name:missing|collection date:missing", "b14", "The difference in the number of alternative splicing events between groups was analyzed using rMATS version 4.1.0 Assembly: GRCz11 Supplementary files format and content: Gene expression matrix", "embryo", null, "Embryos were collected at the 10 somite stage and gently transferred into lysis buffer. Reverse transcription was performed using a SMARTer Ultra Low RNA Kit Clontech  634437 directly from the cell lysates. The cDNA library was prepared using an Advantage 2 PCR Kit Clontech\uff0c639206 and then sequenced via the Illumina sequencing platform NovaSeq 6000.", null, "tissue:embryo|genotype:heterozygous", "GSM8984757", "GSM8984757: b14; Danio rerio; RNA Seq", "GSM8984757 r1", "GSM8984757", "1", "Embryos were collected at the 10 somite stage and gently transferred into lysis buffer. Reverse transcription was performed using a SMARTer Ultra Low RNA Kit Clontech  634437 directly from the cell lysates. The cDNA library was prepared using an Advantage 2 PCR Kit Clontech\uff0c639206 and then sequenced via the Illumina sequencing platform NovaSeq 6000.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP585332", null, null, "b14_1.fq.gz b14_2.fq.gz", "fastq fastq", 19276565400.0, 64255218.0, "GSM8984757 r1", "0:150 1:150", "A:5518694219;C:3928662779;G:4574767411;T:5253904649;N:536342", 150, 150, null, null, 5518694219, 3928662779, 4574767411, 5253904649, 536342, "SRX28800977", "SRS25038275", "SRA2129895", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "China", "2025-05-14", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36213, "SRR33570993", "SRX28800976", "SRS25038274", "SRP585332", "PRJNA1262902", "BCAS2 promotes primitive hematopoiesis by sequestering \u00df catenin within the nucleus", "GSE297155", "Transcriptome Analysis", "Breast carcinoma amplified sequence 2 BCAS2  a core component of the hPrP19 complex  plays crucial roles in various physiological and pathological processes. However  whether BCAS2 has functions other than being a key RNA splicing regulator within the nucleus remains unknown. Here  we show that BCAS2 is essential for primitive hematopoiesis in zebrafish and mouse embryos. The activation of Wnt/\u00df catenin signal  which is required for hematopoietic progenitor differentiation  is significantly decreased upon depletion of bcas2 in zebrafish embryos and mouse embryonic fibroblasts MEFs. Interestingly  BCAS2 de?ciency has no obvious impact on the splicing efficiency of \u00df catenin pre mRNA  while significantly attenuating \u00df catenin nuclear accumulation. Moreover  we find that BCAS2 directly binds to \u00df catenin via its coiled coil domains  thereby sequestering \u00df catenin within the nucleus. Thus  our results uncover a previously unknown function of BCAS2 in promoting Wnt signaling by enhancing \u00df catenin nuclear retention during primitive hematopoiesis. Overall design: RNA sequencing profiling for wild type and bcas2 +/?14 embryos at 10 ss.", null, null, null, "b1", "GSM8984756", null, "source name:embryo|tissue:embryo|genotype:WT|geo loc name:missing|collection date:missing", "b1", "The difference in the number of alternative splicing events between groups was analyzed using rMATS version 4.1.0 Assembly: GRCz11 Supplementary files format and content: Gene expression matrix", "embryo", null, "Embryos were collected at the 10 somite stage and gently transferred into lysis buffer. Reverse transcription was performed using a SMARTer Ultra Low RNA Kit Clontech  634437 directly from the cell lysates. The cDNA library was prepared using an Advantage 2 PCR Kit Clontech\uff0c639206 and then sequenced via the Illumina sequencing platform NovaSeq 6000.", null, "tissue:embryo|genotype:WT", "GSM8984756", "GSM8984756: b1; Danio rerio; RNA Seq", "GSM8984756 r1", "GSM8984756", "1", "Embryos were collected at the 10 somite stage and gently transferred into lysis buffer. Reverse transcription was performed using a SMARTer Ultra Low RNA Kit Clontech  634437 directly from the cell lysates. The cDNA library was prepared using an Advantage 2 PCR Kit Clontech\uff0c639206 and then sequenced via the Illumina sequencing platform NovaSeq 6000.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP585332", null, null, "b1_1.fq.gz b1_2.fq.gz", "fastq fastq", 11343837000.0, 37812790.0, "GSM8984756 r1", "0:150 1:150", "A:3221434300;C:2431571093;G:2554438872;T:3136077724;N:315011", 150, 150, null, null, 3221434300, 2431571093, 2554438872, 3136077724, 315011, "SRX28800976", "SRS25038274", "SRA2129895", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "China", "2025-05-14", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36406, "SRR546819", "SRX180749", "SRS347211", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 14 somites stage", "D. rerio 14 somites embryo", "D. rerio 14 somites embryo", null, null, null, null, null, null, null, null, null, null, "RNAseq   D. rerio 14 somites embryo", "RNAseq   D. rerio 14 somites embryo", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "RNAseq_14somites_2.fastq", "fastq", 2976465520.0, 19582010.0, "RNAseq   D. rerio 14 somites embryo", "0:76 1:76", "A:747831748;C:733533938;G:754151936;T:738091995;N:2855903", 76, 76, null, null, 747831748, 733533938, 754151936, 738091995, 2855903, "SRX180749", "SRS347211", "SRA055273", "University of Bergen", "ZEPROME consortium", 2, 0.9236, 0.91427, 0.0861, 0.08534, 0.7559, 0.75528, 0.48428, 0.47549, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2015-07-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36412, "SRR516557", "SRX156352", "SRS347211", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 14 somites stage", "D. rerio 14 somites embryo", "D. rerio 14 somites embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio 14 somites embryo", "CAGE   D. rerio 14 somites embryo run2", "D. rerio 14 somites embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 73689048.0, 2729224.0, "CAGE   D. rerio 14 somites embryo run1", "0:27", "A:19506796;C:16238588;G:21636330;T:16307334;N:0", 27, null, null, null, 19506796, 16238588, 21636330, 16307334, 0, "SRX156352", "SRS347211", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.63348, null, 0.09461, null, 0.76199, null, 0.68697, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36413, "SRR516558", "SRX156352", "SRS347211", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 14 somites stage", "D. rerio 14 somites embryo", "D. rerio 14 somites embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio 14 somites embryo", "CAGE   D. rerio 14 somites embryo run2", "D. rerio 14 somites embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_14somites_run2.fastq", "fastq", 212381811.0, 7865993.0, "CAGE   D. rerio 14 somites embryo run2", "0:27", "A:53780820;C:47467464;G:59893810;T:51239717;N:0", 27, null, null, null, 53780820, 47467464, 59893810, 51239717, 0, "SRX156352", "SRS347211", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.5278, null, 0.0806, null, 0.77589, null, 0.72881, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36670, "SRR797919", "SRX255755", "SRS404586", "SRP020090", "PRJNA194542", "Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish", "GSE45532", "Transcriptome Analysis", "The basic helix loop helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes  including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets  in particular fast twitch muscle differentiation genes  thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast twitch muscle specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber type regulator  Prdm1a  a SET domain DNA binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype  early and increased fast muscle differentiation  is the opposite of the Pbx null phenotype  delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes  we used RNA seq analysis to globally assess gene expression in zebrafish embryos with single  and double losses of function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4 MO;prdm1a /  embryos  suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However  other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus  our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program. Overall design: Total RNA samples were genotyped and pooled for 4 sample types: control MO;prdm1+/+; control MO;prdm1 / ; pbx2/4 MO;prdm1+/+; and pbx2/4 MO;prdm1 /  embryos at the 10 somite s stage from three independent sets of egg collections/injections.", null, "pubmed:23789105", null, "pbx2/4 MO; prdm1 /  rep3", "GSM1108126", null, "tissue:embryos|developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1 / ", "pbx2/4 MO; prdm1 /  rep3", "Reads were aligned by tophat 1.4 gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence. differentential gene expression detection was performed by edgeR. Genome build: Zv9 release 63 Supplementary files format and content: GSE45532 gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes.  Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name  ENSEMBL ID  and read counts for all samples. Supplementary files format and content: GSE45532 double.genes.csv:  Differential expressed genes between Double knockout pbx2/4 MO;prdm1 /  vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 pbx.genes.csv: Differential expressed genes between pbx2/4 MO vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 prdm.genes.csv: Differential expressed genes between prom1 /  vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff.  The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change.", "embryos", "Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.", "Total RNA from individual embryos was isolated using the RNAqueous Micro Kit Ambion. Samples were genotyped  pooled  then further cleaned and concentrated using the RNeasy MinElute Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1 / ", "GSM1108126", "GSM1108126: pbx2/4 MO; prdm1 /  rep3; Danio rerio; RNA Seq", "GSM1108126 1", null, "1", null, "GEO Accession:GSM1108126", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP020090", null, null, "LM4_3pbxAMA_TGACCA_L005_R1_001.fastq.gz LM4_3pbxAMA_TGACCA_L005_R1_002.fastq.gz LM4_3pbxAMA_TGACCA_L005_R1_003.fastq.gz LM4_3pbxAMA_TGACCA_L005_R1_004.fastq.gz LM4_3pbxAMA_TGACCA_L005_R1_005.fastq.gz LM4_3pbxAMA_TGACCA_L005_R1_006.fastq.gz LM4_3pbxAMA_TGACCA_L005_R1_007.fastq.gz LM4_3pbxAMA_TGACCA_L005_R1_009.fastq.gz LM4_3pbxAMA_TGACCA_L005_R1_008.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq fastq", 3357724887.0, 33916413.0, "GSM1108126 r1", "0:99", "A:867535436;C:806347044;G:804849580;T:864830356;N:14162471", 99, null, null, null, 867535436, 806347044, 804849580, 864830356, 14162471, "SRX255755", "SRS404586", "SRA071780", "GEO", "Tapscott, Human Biology, Fred Hutchison Cancer Research Center", 1, 0.9452, null, 0.1061, null, 0.72139, null, 0.47965, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36671, "SRR797918", "SRX255754", "SRS404585", "SRP020090", "PRJNA194542", "Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish", "GSE45532", "Transcriptome Analysis", "The basic helix loop helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes  including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets  in particular fast twitch muscle differentiation genes  thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast twitch muscle specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber type regulator  Prdm1a  a SET domain DNA binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype  early and increased fast muscle differentiation  is the opposite of the Pbx null phenotype  delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes  we used RNA seq analysis to globally assess gene expression in zebrafish embryos with single  and double losses of function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4 MO;prdm1a /  embryos  suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However  other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus  our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program. Overall design: Total RNA samples were genotyped and pooled for 4 sample types: control MO;prdm1+/+; control MO;prdm1 / ; pbx2/4 MO;prdm1+/+; and pbx2/4 MO;prdm1 /  embryos at the 10 somite s stage from three independent sets of egg collections/injections.", null, "pubmed:23789105", null, "pbx2/4 MO; prdm1 /  rep2", "GSM1108125", null, "tissue:embryos|developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1 / ", "pbx2/4 MO; prdm1 /  rep2", "Reads were aligned by tophat 1.4 gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence. differentential gene expression detection was performed by edgeR. Genome build: Zv9 release 63 Supplementary files format and content: GSE45532 gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes.  Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name  ENSEMBL ID  and read counts for all samples. Supplementary files format and content: GSE45532 double.genes.csv:  Differential expressed genes between Double knockout pbx2/4 MO;prdm1 /  vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 pbx.genes.csv: Differential expressed genes between pbx2/4 MO vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 prdm.genes.csv: Differential expressed genes between prom1 /  vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff.  The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change.", "embryos", "Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.", "Total RNA from individual embryos was isolated using the RNAqueous Micro Kit Ambion. Samples were genotyped  pooled  then further cleaned and concentrated using the RNeasy MinElute Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1 / ", "GSM1108125", "GSM1108125: pbx2/4 MO; prdm1 /  rep2; Danio rerio; RNA Seq", "GSM1108125 1", null, "1", null, "GEO Accession:GSM1108125", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP020090", null, null, "LM8-zfdoublea_CTTGTA_L004_R1_001.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_002.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_003.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_004.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_005.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_006.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_007.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_008.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_009.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_010.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_012.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_013.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_014.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_015.fastq.gz LM8-zfdoublea_CTTGTA_L004_R1_011.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 5666953347.0, 57241953.0, "GSM1108125 r1", "0:99", "A:1495994269;C:1330901018;G:1331802450;T:1489768715;N:18486895", 99, null, null, null, 1495994269, 1330901018, 1331802450, 1489768715, 18486895, "SRX255754", "SRS404585", "SRA071780", "GEO", "Tapscott, Human Biology, Fred Hutchison Cancer Research Center", 1, 0.94561, null, 0.08762, null, 0.72109, null, 0.47406, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36672, "SRR797917", "SRX255753", "SRS404584", "SRP020090", "PRJNA194542", "Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish", "GSE45532", "Transcriptome Analysis", "The basic helix loop helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes  including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets  in particular fast twitch muscle differentiation genes  thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast twitch muscle specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber type regulator  Prdm1a  a SET domain DNA binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype  early and increased fast muscle differentiation  is the opposite of the Pbx null phenotype  delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes  we used RNA seq analysis to globally assess gene expression in zebrafish embryos with single  and double losses of function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4 MO;prdm1a /  embryos  suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However  other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus  our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program. Overall design: Total RNA samples were genotyped and pooled for 4 sample types: control MO;prdm1+/+; control MO;prdm1 / ; pbx2/4 MO;prdm1+/+; and pbx2/4 MO;prdm1 /  embryos at the 10 somite s stage from three independent sets of egg collections/injections.", null, "pubmed:23789105", null, "pbx2/4 MO; prdm1 /  rep1", "GSM1108124", null, "tissue:embryos|developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1 / ", "pbx2/4 MO; prdm1 /  rep1", "Reads were aligned by tophat 1.4 gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence. differentential gene expression detection was performed by edgeR. Genome build: Zv9 release 63 Supplementary files format and content: GSE45532 gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes.  Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name  ENSEMBL ID  and read counts for all samples. Supplementary files format and content: GSE45532 double.genes.csv:  Differential expressed genes between Double knockout pbx2/4 MO;prdm1 /  vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 pbx.genes.csv: Differential expressed genes between pbx2/4 MO vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 prdm.genes.csv: Differential expressed genes between prom1 /  vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff.  The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change.", "embryos", "Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.", "Total RNA from individual embryos was isolated using the RNAqueous Micro Kit Ambion. Samples were genotyped  pooled  then further cleaned and concentrated using the RNeasy MinElute Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1 / ", "GSM1108124", "GSM1108124: pbx2/4 MO; prdm1 /  rep1; Danio rerio; RNA Seq", "GSM1108124 1", null, "1", null, "GEO Accession:GSM1108124", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP020090", null, null, "LM8_prdm1pbx_ACTTGA_L006_R1_001.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_002.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_003.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_004.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_005.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_008.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_007.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_006.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq", 2850641541.0, 28794359.0, "GSM1108124 r1", "0:99", "A:734323874;C:687104792;G:685405933;T:731354277;N:12452665", 99, null, null, null, 734323874, 687104792, 685405933, 731354277, 12452665, "SRX255753", "SRS404584", "SRA071780", "GEO", "Tapscott, Human Biology, Fred Hutchison Cancer Research Center", 1, 0.94396, null, 0.11137, null, 0.72308, null, 0.49037, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36673, "SRR797916", "SRX255752", "SRS404583", "SRP020090", "PRJNA194542", "Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish", "GSE45532", "Transcriptome Analysis", "The basic helix loop helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes  including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets  in particular fast twitch muscle differentiation genes  thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast twitch muscle specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber type regulator  Prdm1a  a SET domain DNA binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype  early and increased fast muscle differentiation  is the opposite of the Pbx null phenotype  delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes  we used RNA seq analysis to globally assess gene expression in zebrafish embryos with single  and double losses of function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4 MO;prdm1a /  embryos  suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However  other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus  our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program. Overall design: Total RNA samples were genotyped and pooled for 4 sample types: control MO;prdm1+/+; control MO;prdm1 / ; pbx2/4 MO;prdm1+/+; and pbx2/4 MO;prdm1 /  embryos at the 10 somite s stage from three independent sets of egg collections/injections.", null, "pubmed:23789105", null, "pbx2/4 MO rep3", "GSM1108123", null, "tissue:embryos|developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1+/+", "pbx2/4 MO rep3", "Reads were aligned by tophat 1.4 gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence. differentential gene expression detection was performed by edgeR. Genome build: Zv9 release 63 Supplementary files format and content: GSE45532 gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes.  Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name  ENSEMBL ID  and read counts for all samples. Supplementary files format and content: GSE45532 double.genes.csv:  Differential expressed genes between Double knockout pbx2/4 MO;prdm1 /  vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 pbx.genes.csv: Differential expressed genes between pbx2/4 MO vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 prdm.genes.csv: Differential expressed genes between prom1 /  vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff.  The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change.", "embryos", "Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.", "Total RNA from individual embryos was isolated using the RNAqueous Micro Kit Ambion. Samples were genotyped  pooled  then further cleaned and concentrated using the RNeasy MinElute Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1+/+", "GSM1108123", "GSM1108123: pbx2/4 MO rep3; Danio rerio; RNA Seq", "GSM1108123 1", null, "1", null, "GEO Accession:GSM1108123", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP020090", null, null, "LM3_3pbxAWA_ATGTCA_L005_R1_001.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_002.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_003.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_004.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_005.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_006.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_007.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_008.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_009.fastq.gz LM3_3pbxAWA_ATGTCA_L005_R1_010.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 3637876671.0, 36746229.0, "GSM1108123 r1", "0:99", "A:946027780;C:867852983;G:866870491;T:941694055;N:15431362", 99, null, null, null, 946027780, 867852983, 866870491, 941694055, 15431362, "SRX255752", "SRS404583", "SRA071780", "GEO", "Tapscott, Human Biology, Fred Hutchison Cancer Research Center", 1, 0.94518, null, 0.10825, null, 0.71875, null, 0.47778, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36674, "SRR797915", "SRX255751", "SRS404582", "SRP020090", "PRJNA194542", "Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish", "GSE45532", "Transcriptome Analysis", "The basic helix loop helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes  including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets  in particular fast twitch muscle differentiation genes  thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast twitch muscle specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber type regulator  Prdm1a  a SET domain DNA binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype  early and increased fast muscle differentiation  is the opposite of the Pbx null phenotype  delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes  we used RNA seq analysis to globally assess gene expression in zebrafish embryos with single  and double losses of function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4 MO;prdm1a /  embryos  suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However  other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus  our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program. Overall design: Total RNA samples were genotyped and pooled for 4 sample types: control MO;prdm1+/+; control MO;prdm1 / ; pbx2/4 MO;prdm1+/+; and pbx2/4 MO;prdm1 /  embryos at the 10 somite s stage from three independent sets of egg collections/injections.", null, "pubmed:23789105", null, "pbx2/4 MO rep2", "GSM1108122", null, "tissue:embryos|developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1+/+", "pbx2/4 MO rep2", "Reads were aligned by tophat 1.4 gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence. differentential gene expression detection was performed by edgeR. Genome build: Zv9 release 63 Supplementary files format and content: GSE45532 gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes.  Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name  ENSEMBL ID  and read counts for all samples. Supplementary files format and content: GSE45532 double.genes.csv:  Differential expressed genes between Double knockout pbx2/4 MO;prdm1 /  vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 pbx.genes.csv: Differential expressed genes between pbx2/4 MO vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 prdm.genes.csv: Differential expressed genes between prom1 /  vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff.  The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change.", "embryos", "Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.", "Total RNA from individual embryos was isolated using the RNAqueous Micro Kit Ambion. Samples were genotyped  pooled  then further cleaned and concentrated using the RNeasy MinElute Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1+/+", "GSM1108122", "GSM1108122: pbx2/4 MO rep2; Danio rerio; RNA Seq", "GSM1108122 1", null, "1", null, "GEO Accession:GSM1108122", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP020090", null, null, "LM7-zfpbxa_CAGATC_L004_R1_002.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_004.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_007.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_008.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_009.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_010.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_011.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_012.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_013.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_014.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_006.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_005.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_003.fastq.gz LM7-zfpbxa_CAGATC_L004_R1_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 5511604032.0, 55672768.0, "GSM1108122 r1", "0:99", "A:1455673819;C:1294873116;G:1297543997;T:1445963138;N:17549962", 99, null, null, null, 1455673819, 1294873116, 1297543997, 1445963138, 17549962, "SRX255751", "SRS404582", "SRA071780", "GEO", "Tapscott, Human Biology, Fred Hutchison Cancer Research Center", 1, 0.94369, null, 0.09971, null, 0.72506, null, 0.47551, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-03-27", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36675, "SRR797914", "SRX255750", "SRS404581", "SRP020090", "PRJNA194542", "Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish", "GSE45532", "Transcriptome Analysis", "The basic helix loop helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes  including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets  in particular fast twitch muscle differentiation genes  thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast twitch muscle specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber type regulator  Prdm1a  a SET domain DNA binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype  early and increased fast muscle differentiation  is the opposite of the Pbx null phenotype  delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes  we used RNA seq analysis to globally assess gene expression in zebrafish embryos with single  and double losses of function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4 MO;prdm1a /  embryos  suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However  other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus  our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program. Overall design: Total RNA samples were genotyped and pooled for 4 sample types: control MO;prdm1+/+; control MO;prdm1 / ; pbx2/4 MO;prdm1+/+; and pbx2/4 MO;prdm1 /  embryos at the 10 somite s stage from three independent sets of egg collections/injections.", null, "pubmed:23789105", null, "pbx2/4 MO rep1", "GSM1108121", null, "tissue:embryos|developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1+/+", "pbx2/4 MO rep1", "Reads were aligned by tophat 1.4 gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence. differentential gene expression detection was performed by edgeR. Genome build: Zv9 release 63 Supplementary files format and content: GSE45532 gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes.  Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name  ENSEMBL ID  and read counts for all samples. Supplementary files format and content: GSE45532 double.genes.csv:  Differential expressed genes between Double knockout pbx2/4 MO;prdm1 /  vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 pbx.genes.csv: Differential expressed genes between pbx2/4 MO vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change. Supplementary files format and content: GSE45532 prdm.genes.csv: Differential expressed genes between prom1 /  vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff.  The columns are gene name  ENSEMBL gene.id  edgeR pvalue  edgeR log fold change.", "embryos", "Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.", "Total RNA from individual embryos was isolated using the RNAqueous Micro Kit Ambion. Samples were genotyped  pooled  then further cleaned and concentrated using the RNeasy MinElute Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:10 somites|strain:AB|genotype:pbx2/4 MO; prdm1+/+", "GSM1108121", "GSM1108121: pbx2/4 MO rep1; Danio rerio; RNA Seq", "GSM1108121 1", null, "1", null, "GEO Accession:GSM1108121", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP020090", null, null, "LM7_1pbx_CAGATC_L006_R1_001.fastq.gz LM7_1pbx_CAGATC_L006_R1_002.fastq.gz LM7_1pbx_CAGATC_L006_R1_003.fastq.gz LM7_1pbx_CAGATC_L006_R1_004.fastq.gz LM7_1pbx_CAGATC_L006_R1_005.fastq.gz LM7_1pbx_CAGATC_L006_R1_006.fastq.gz LM7_1pbx_CAGATC_L006_R1_007.fastq.gz LM7_1pbx_CAGATC_L006_R1_008.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq", 3147482646.0, 31792754.0, "GSM1108121 r1", "0:99", "A:810993548;C:759638223;G:757885275;T:805243586;N:13722014", 99, null, null, null, 810993548, 759638223, 757885275, 805243586, 13722014, "SRX255750", "SRS404581", "SRA071780", "GEO", "Tapscott, Human 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