{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\"", "rows": [[9898, "ERR4194114", "ERX4155254", "ERS4601292", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. 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For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. 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For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. 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For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. 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For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 1", "SAMEA6873728", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873728|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 1|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 1 s", "Sample 1 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:6|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA6h_1_S1_L001.bam", "bam", 7181772357.0, 71106657.0, "E MTAB 9193:cDNA6h 1 S1 L001", "0:101", "A:2074032710;C:1415439071;G:1544274166;T:2140112533;N:7913877", 101, null, null, null, 2074032710, 1415439071, 1544274166, 2140112533, 7913877, "ERX4155253", "ERS4601291", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.9297, null, 0.12156, null, 0.8117, null, 0.51457, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9901, "ERR4194113", "ERX4155253", "ERS4601291", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 1", "SAMEA6873728", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873728|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 1|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 1 s", "Sample 1 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:6|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA6h_1_S1_L002.bam", "bam", 7256542253.0, 71846953.0, "E MTAB 9193:cDNA6h 1 S1 L002", "0:101", "A:2096163385;C:1430325700;G:1560530043;T:2162265616;N:7257509", 101, null, null, null, 2096163385, 1430325700, 1560530043, 2162265616, 7257509, "ERX4155253", "ERS4601291", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.92882, null, 0.12127, null, 0.81162, null, 0.51457, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9902, "ERR4194128", "ERX4155256", "ERS4601294", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 4", "SAMEA6873731", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873731|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 4|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 4|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 4 s", "Sample 4 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:13|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA13h_1_control_S1_L001.bam", "bam", 10785974123.0, 106791823.0, "E MTAB 9193:cDNA13h 1 control S1 L001", "0:101", "A:3007305661;C:2241057062;G:2505494392;T:2986021199;N:46095809", 101, null, null, null, 3007305661, 2241057062, 2505494392, 2986021199, 46095809, "ERX4155256", "ERS4601294", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.67094, null, 0.07571, null, 0.92951, null, 0.5272, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9903, "ERR4194129", "ERX4155256", "ERS4601294", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 4", "SAMEA6873731", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873731|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 4|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 4|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 4 s", "Sample 4 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:13|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA13h_1_control_S1_L002.bam", "bam", 10595192294.0, 104902894.0, "E MTAB 9193:cDNA13h 1 control S1 L002", "0:101", "A:2971916419;C:2204229263;G:2390854035;T:2949877754;N:78314823", 101, null, null, null, 2971916419, 2204229263, 2390854035, 2949877754, 78314823, "ERX4155256", "ERS4601294", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.67255, null, 0.08054, null, 0.91583, null, 0.52661, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9904, "ERR4194116", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_1_S3_L001.bam", "bam", 1622536412.0, 16556494.0, "E MTAB 9193:cDNA10h 1 S3 L001", "0:98", "A:491141175;C:317161060;G:354179755;T:459976409;N:78013", 98, null, null, null, 491141175, 317161060, 354179755, 459976409, 78013, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93238, null, 0.13033, null, 0.89132, null, 0.47076, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9905, "ERR4194117", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_1_S3_L002.bam", "bam", 1484328776.0, 15146212.0, "E MTAB 9193:cDNA10h 1 S3 L002", "0:98", "A:450782055;C:290088574;G:322801188;T:420570801;N:86158", 98, null, null, null, 450782055, 290088574, 322801188, 420570801, 86158, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.92846, null, 0.13128, null, 0.89923, null, 0.46879, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9906, "ERR4194118", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_1_S3_L003.bam", "bam", 1578833116.0, 16110542.0, "E MTAB 9193:cDNA10h 1 S3 L003", "0:98", "A:477600666;C:308260969;G:347303289;T:445467384;N:200808", 98, null, null, null, 477600666, 308260969, 347303289, 445467384, 200808, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93107, null, 0.12965, null, 0.91265, null, 0.47375, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9907, "ERR4194119", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_1_S3_L004.bam", "bam", 1859564994.0, 18975153.0, "E MTAB 9193:cDNA10h 1 S3 L004", "0:98", "A:562936790;C:364057256;G:406607636;T:525811595;N:151717", 98, null, null, null, 562936790, 364057256, 406607636, 525811595, 151717, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93453, null, 0.1266, null, 0.87714, null, 0.46957, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9908, "ERR4194120", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_2_S3_L001.bam", "bam", 1156341102.0, 11799399.0, "E MTAB 9193:cDNA10h 2 S3 L001", "0:98", "A:345857612;C:224453195;G:257551986;T:327969064;N:509245", 98, null, null, null, 345857612, 224453195, 257551986, 327969064, 509245, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93863, null, 0.10744, null, 0.81984, null, 0.501, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9909, "ERR4194121", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_2_S3_L002.bam", "bam", 1105219696.0, 11277752.0, "E MTAB 9193:cDNA10h 2 S3 L002", "0:98", "A:331051973;C:214369903;G:246546338;T:312897773;N:353709", 98, null, null, null, 331051973, 214369903, 246546338, 312897773, 353709, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93941, null, 0.10818, null, 0.82211, null, 0.50079, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9910, "ERR4194122", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_2_S3_L003.bam", "bam", 1105199606.0, 11277547.0, "E MTAB 9193:cDNA10h 2 S3 L003", "0:98", "A:331158619;C:214305131;G:246465559;T:312930408;N:339889", 98, null, null, null, 331158619, 214305131, 246465559, 312930408, 339889, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93767, null, 0.10645, null, 0.82329, null, 0.50057, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9911, "ERR4194123", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_2_S3_L004.bam", "bam", 1108707712.0, 11313344.0, "E MTAB 9193:cDNA10h 2 S3 L004", "0:98", "A:331374433;C:215925150;G:247131942;T:313865174;N:411013", 98, null, null, null, 331374433, 215925150, 247131942, 313865174, 411013, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93827, null, 0.10842, null, 0.82031, null, 0.49241, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9912, "ERR4194124", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_2_S3_L005.bam", "bam", 1110084612.0, 11327394.0, "E MTAB 9193:cDNA10h 2 S3 L005", "0:98", "A:332881960;C:215360330;G:247563319;T:313842331;N:436672", 98, null, null, null, 332881960, 215360330, 247563319, 313842331, 436672, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93827, null, 0.10719, null, 0.8238, null, 0.50406, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9913, "ERR4194125", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_2_S3_L006.bam", "bam", 1113812728.0, 11365436.0, "E MTAB 9193:cDNA10h 2 S3 L006", "0:98", "A:333112288;C:216649152;G:248341020;T:315338848;N:371420", 98, null, null, null, 333112288, 216649152, 248341020, 315338848, 371420, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93843, null, 0.10675, null, 0.82079, null, 0.49284, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9914, "ERR4194126", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_2_S3_L007.bam", "bam", 1119495748.0, 11423426.0, "E MTAB 9193:cDNA10h 2 S3 L007", "0:98", "A:335288339;C:217283719;G:249624836;T:316900388;N:398466", 98, null, null, null, 335288339, 217283719, 249624836, 316900388, 398466, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93711, null, 0.10749, null, 0.82266, null, 0.49382, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9915, "ERR4194127", "ERX4155255", "ERS4601293", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 3", "SAMEA6873730", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 3 s", "Sample 3 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:10|Experimental Factor: RNA interference:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA10h_2_S3_L008.bam", "bam", 1175946688.0, 11999456.0, "E MTAB 9193:cDNA10h 2 S3 L008", "0:98", "A:351364169;C:228318193;G:261971072;T:333863943;N:429311", 98, null, null, null, 351364169, 228318193, 261971072, 333863943, 429311, "ERX4155255", "ERS4601293", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93851, null, 0.10755, null, 0.82158, null, 0.49895, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9916, "ERR4194130", "ERX4155257", "ERS4601295", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 5", "SAMEA6873732", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873732|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 5|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 5|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 5 s", "Sample 5 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:13|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA13h_2_gata56KD_S2_L001.bam", "bam", 7791309377.0, 77141677.0, "E MTAB 9193:cDNA13h 2 gata56KD S2 L001", "0:101", "A:2198242220;C:1593746618;G:1784167452;T:2181979820;N:33173267", 101, null, null, null, 2198242220, 1593746618, 1784167452, 2181979820, 33173267, "ERX4155257", "ERS4601295", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.66736, null, 0.08039, null, 0.93026, null, 0.50796, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9917, "ERR4194131", "ERX4155257", "ERS4601295", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Sample 5", "SAMEA6873732", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873732|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 5|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 5|scientific name:Danio rerio|sex:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E MTAB 9193:Sample 5 s", "Sample 5 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\u2009\u03bcl calcium free Ringer solution 116\u2009mM NaCl  2.6\u2009mM KCl  5\u2009mM HEPE  pH 7.0 for 5\u2009min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100\u2009\u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.", "Experimental Factor: age:13|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP122151", "Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", "cDNA13h_2_gata56KD_S2_L002.bam", "bam", 7658149967.0, 75823267.0, "E MTAB 9193:cDNA13h 2 gata56KD S2 L002", "0:101", "A:2172230233;C:1568805100;G:1703587704;T:2157181071;N:56345859", 101, null, null, null, 2172230233, 1568805100, 1703587704, 2157181071, 56345859, "ERX4155257", "ERS4601295", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.66565, null, 0.08597, null, 0.91804, null, 0.51772, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2020-06-04", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10060, "ERR4795364", "ERX4665135", "ERS5281176", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Sample 4", "E MTAB 9727:Sample 4", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 4 s", "Sample 4 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 4", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz", "fastq", 5410723202.0, 71707309.0, "E MTAB 9727:Sample 4", "0:75.46 1:0", "A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666", 75, 0, null, null, 1330416803, 531269504, 734031980, 2814959249, 45666, "ERX4665135", "ERS5281176", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.33614, null, 0.21532, null, 0.99019, null, 0.41002, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10061, "ERR4795365", "ERX4665135", "ERS5281176", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Sample 4", "E MTAB 9727:Sample 4", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 4 s", "Sample 4 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 4", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz", "fastq", 5414184547.0, 71707309.0, "E MTAB 9727:Sample 4 1", "0:0 1:75.50", "A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967", 0, 75, null, null, 1582938104, 1052565419, 1177180395, 1600161662, 1338967, "ERX4665135", "ERS5281176", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.84976, null, 0.28521, null, 0.85038, null, 0.5124, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10062, "ERR4795362", "ERX4665134", "ERS5281175", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Sample 3", "E MTAB 9727:Sample 3", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 3 s", "Sample 3 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 3", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz", "fastq", 4823193891.0, 63965519.0, "E MTAB 9727:Sample 3", "0:75.40 1:0", "A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086", 75, 0, null, null, 1323978162, 446831209, 581746343, 2470114091, 524086, "ERX4665134", "ERS5281175", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.36549, null, 0.19722, null, 0.95552, null, 0.4702, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10063, "ERR4795363", "ERX4665134", "ERS5281175", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Sample 3", "E MTAB 9727:Sample 3", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 3 s", "Sample 3 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 3", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz", "fastq", 4828889391.0, 63965519.0, "E MTAB 9727:Sample 3 1", "0:0 1:75.49", "A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756", 0, 75, null, null, 1434099697, 964508763, 893584575, 1534727600, 1968756, "ERX4665134", "ERS5281175", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.85811, null, 0.26231, null, 0.82731, null, 0.48618, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10064, "ERR4795360", "ERX4665133", "ERS5281174", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Sample 2", "E MTAB 9727:Sample 2", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 2 s", "Sample 2 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 2", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz", "fastq", 5598371393.0, 74235388.0, "E MTAB 9727:Sample 2", "0:75.41 1:0", "A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655", 75, 0, null, null, 1526486973, 558020193, 717587491, 2795646081, 630655, "ERX4665133", "ERS5281174", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.28059, null, 0.19252, null, 0.96404, null, 0.4874, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10065, "ERR4795361", "ERX4665133", "ERS5281174", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Sample 2", "E MTAB 9727:Sample 2", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 2 s", "Sample 2 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 2", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz", "fastq", 5600151371.0, 74235388.0, "E MTAB 9727:Sample 2 1", "0:0 1:75.44", "A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060", 0, 75, null, null, 1850568176, 1035622971, 1071138281, 1640475883, 2346060, "ERX4665133", "ERS5281174", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.7679, null, 0.30371, null, 0.82651, null, 0.43401, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10066, "ERR4795358", "ERX4665132", "ERS5281173", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Sample 1", "E MTAB 9727:Sample 1", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 1 s", "Sample 1 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz", "fastq", 4996502316.0, 66258508.0, "E MTAB 9727:Sample 1", "0:75.41 1:0", "A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936", 75, 0, null, null, 1330744174, 451622042, 591151500, 2622422664, 561936, "ERX4665132", "ERS5281173", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.29754, null, 0.17671, null, 0.9669, null, 0.45463, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10067, "ERR4795359", "ERX4665132", "ERS5281173", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Sample 1", "E MTAB 9727:Sample 1", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 1 s", "Sample 1 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at \u221280\u00b0C.  In brief  ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz", "fastq", 4999908389.0, 66258508.0, "E MTAB 9727:Sample 1 1", "0:0 1:75.46", "A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512", 0, 75, null, null, 1591945117, 933968124, 986108614, 1485824022, 2062512, "ERX4665132", "ERS5281173", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.81333, null, 0.2466, null, 0.83027, null, 0.51572, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11130, "ERR9979395", "ERX9520370", "ERS12499848", "ERP139765", "PRJEB54901", "Single cell RNA sequencing of germ free zebrafish embryos", "E-MTAB-11984", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", null, "Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 2 WT GO+BA", "SAMEA110401656", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "E MTAB 11984:Sample 2 WT GO+BA p", "Sample 2 WT GO+BA p", "Single cell RNA sequencing of germ free zebrafish embryos", "The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139765", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", "P22202_7002_S2_L002_R1_001.fastq.gz P22202_7002_S2_L002_R2_001.fastq.gz", "fastq fastq", 18144406998.0, 153766161.0, "E MTAB 11984:P22202 7002 S2 L002", "0:28 1:90", "A:5277424121;C:3880928155;G:4118706097;T:4866649878;N:698747", 28, 90, null, null, 5277424121, 3880928155, 4118706097, 4866649878, 698747, "ERX9520370", "ERS12499848", "ERA16483151", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.0109, 0.90145, 0.0053, 0.21373, 0.98746, 0.79423, 0.41198, 0.54447, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-22", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11131, "ERR9979394", "ERX9520370", "ERS12499848", "ERP139765", "PRJEB54901", "Single cell RNA sequencing of germ free zebrafish embryos", "E-MTAB-11984", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", null, "Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 2 WT GO+BA", "SAMEA110401656", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "E MTAB 11984:Sample 2 WT GO+BA p", "Sample 2 WT GO+BA p", "Single cell RNA sequencing of germ free zebrafish embryos", "The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139765", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", "P22202_7002_S2_L001_R1_001.fastq.gz P22202_7002_S2_L001_R2_001.fastq.gz", "fastq fastq", 18458951574.0, 156431793.0, "E MTAB 11984:P22202 7002 S2 L001", "0:28 1:90", "A:5372920926;C:3946687814;G:4185647697;T:4953205454;N:489683", 28, 90, null, null, 5372920926, 3946687814, 4185647697, 4953205454, 489683, "ERX9520370", "ERS12499848", "ERA16483151", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.01037, 0.90168, 0.0048, 0.21246, 0.98752, 0.79297, 0.42601, 0.54996, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-22", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11132, "ERR9979392", "ERX9520369", "ERS12499847", "ERP139765", "PRJEB54901", "Single cell RNA sequencing of germ free zebrafish embryos", "E-MTAB-11984", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", null, "Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 1 WT control", "SAMEA110401655", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "E MTAB 11984:Sample 1 WT control p", "Sample 1 WT control p", "Single cell RNA sequencing of germ free zebrafish embryos", "The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:n1", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139765", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", "P22202_7001_S1_L001_R1_001.fastq.gz P22202_7001_S1_L001_R2_001.fastq.gz", "fastq fastq", 19396994226.0, 164381307.0, "E MTAB 11984:P22202 7001 S1 L001", "0:28 1:90", "A:5665199484;C:4091196594;G:4415211076;T:5224866754;N:520318", 28, 90, null, null, 5665199484, 4091196594, 4415211076, 5224866754, 520318, "ERX9520369", "ERS12499847", "ERA16483151", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.01093, 0.89238, 0.00557, 0.232, 0.98764, 0.79444, 0.40806, 0.54781, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-22", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11133, "ERR9979393", "ERX9520369", "ERS12499847", "ERP139765", "PRJEB54901", "Single cell RNA sequencing of germ free zebrafish embryos", "E-MTAB-11984", "Transcriptome Analysis", "The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", null, "Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Sample 1 WT control", "SAMEA110401655", "Institute of Environmental Medicine, Karolinska Institutet", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "E MTAB 11984:Sample 1 WT control p", "Sample 1 WT control p", "Single cell RNA sequencing of germ free zebrafish embryos", "The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 \u03bcg/mL  kanamycin 5 \u03bcg/mL and amphotericin B 250 ng/mL and incubated at 28\u00b0C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28\u00b0C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 \u00b5g/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 \u03bcL of pre warmed enzyme mix containing 460 \u03bcL of 0.25% trypsin EDTA Gibco and 40 \u03bcL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 \u00b0C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 \u03bcL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 \u03bcm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 \u03bcM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 \u00b0C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.", "Experimental Factor: stimulus:n1", "AMPLICON", "TRANSCRIPTOMIC SINGLE CELL", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP139765", "Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos", "ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22", "P22202_7001_S1_L002_R1_001.fastq.gz P22202_7001_S1_L002_R2_001.fastq.gz", "fastq fastq", 19063958224.0, 161558968.0, "E MTAB 11984:P22202 7001 S1 L002", "0:28 1:90", "A:5563588848;C:4022930643;G:4344549562;T:5132136743;N:752428", 28, 90, null, null, 5563588848, 4022930643, 4344549562, 5132136743, 752428, "ERX9520369", "ERS12499847", "ERA16483151", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", "Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive", 2, 0.01118, 0.89308, 0.00573, 0.23128, 0.98737, 0.79354, 0.39264, 0.54552, 28, 90, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "full_length", "size_fractionation", "trueseq", "sc", "single_cell_droplet", "10x", null, "Sweden", "2022-07-22", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11238, "ERR10782555", "ERX10233132", "ERS14439197", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 6", "E MTAB 12503:Sample 6", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 6 p", "Sample 6 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz", "fastq fastq", 14809693138.0, 49038719.0, "E MTAB 12503:20170530.A 6 R", "0:151 1:151", "A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269", 151, 151, null, null, 4069749497, 3367864217, 3430269434, 3928390721, 13419269, "ERX10233132", "ERS14439197", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.83945, 0.69977, 0.27269, 0.22488, 0.74523, 0.77654, 0.4899, 0.4358, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11239, "ERR10782554", "ERX10233131", "ERS14439196", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 5", "E MTAB 12503:Sample 5", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 5 p", "Sample 5 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz", "fastq fastq", 14954968728.0, 49519764.0, "E MTAB 12503:20170530.A 5 R", "0:151 1:151", "A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280", 151, 151, null, null, 4063340262, 3440933120, 3455723079, 3981396987, 13575280, "ERX10233131", "ERS14439196", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.85891, 0.86859, 0.28842, 0.28866, 0.7349, 0.75051, 0.45532, 0.49145, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11240, "ERR10782553", "ERX10233130", "ERS14439195", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 2", "E MTAB 12503:Sample 2", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 2 p", "Sample 2 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz", "fastq fastq", 16267571562.0, 53866131.0, "E MTAB 12503:20170530.A 2 R", "0:151 1:151", "A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668", 151, 151, null, null, 4395815325, 3765428574, 3780844712, 4310729283, 14753668, "ERX10233130", "ERS14439195", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.86977, 0.8727, 0.28497, 0.28427, 0.70763, 0.72301, 0.47478, 0.47986, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11241, "ERR10782552", "ERX10233129", "ERS14439194", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 1", "E MTAB 12503:Sample 1", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 1|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 1 p", "Sample 1 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz", "fastq fastq", 15446599662.0, 51147681.0, "E MTAB 12503:20170530.A 1 R", "0:151 1:151", "A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332", 151, 151, null, null, 4289931639, 3451135010, 3474244788, 4217248893, 14039332, "ERX10233129", "ERS14439194", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.90114, 0.90507, 0.32128, 0.32127, 0.70232, 0.71956, 0.47336, 0.47528, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11242, "ERR10782551", "ERX10233128", "ERS14439193", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 7", "E MTAB 12503:Sample 7", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 7|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 7 p", "Sample 7 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:bud|Experimental Factor: genotype:rbm8a d5/d5", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz", "fastq fastq", 12726557236.0, 42140918.0, "E MTAB 12503:20170530.A 7 R", "0:151 1:151", "A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382", 151, 151, null, null, 3510176970, 2879679978, 2932244172, 3392911734, 11544382, "ERX10233128", "ERS14439193", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.88531, 0.88678, 0.33279, 0.3329, 0.73545, 0.74992, 0.52548, 0.52864, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11243, "ERR10782550", "ERX10233127", "ERS14439192", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 4", "E MTAB 12503:Sample 4", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 4|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 4 p", "Sample 4 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz", "fastq fastq", 15697575554.0, 51978727.0, "E MTAB 12503:20170530.A 4 R", "0:151 1:151", "A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133", 151, 151, null, null, 4256444510, 3622485921, 3650190489, 4154211501, 14243133, "ERX10233127", "ERS14439192", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.87714, 0.88071, 0.29319, 0.29235, 0.69844, 0.7164, 0.47594, 0.47385, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11244, "ERR10782549", "ERX10233126", "ERS14439191", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 3", "E MTAB 12503:Sample 3", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 3|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 3 p", "Sample 3 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz", "fastq fastq", 13839085674.0, 45824787.0, "E MTAB 12503:20170530.A 3 R", "0:151 1:151", "A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362", 151, 151, null, null, 3812423011, 3120168590, 3163957945, 3729983766, 12552362, "ERX10233126", "ERS14439191", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.88987, 0.74432, 0.33651, 0.27875, 0.69229, 0.72934, 0.46981, 0.46116, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11753, "ERR11758614", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S25_L001_R1_001.fastq.gz FliTp124hpf_S25_L001_R2_001.fastq.gz", "fastq fastq", 226833768.0, 1800268.0, "E MTAB 13196:FliTp124hpf S25 L001", "0:28 1:98", "A:65319978;C:50920193;G:49999849;T:60474280;N:119468", 28, 98, null, null, 65319978, 50920193, 49999849, 60474280, 119468, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00122, 0.88236, 0.00056, 0.09684, 0.9978, 0.89309, 0.424, 0.44186, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11754, "ERR11758619", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S27_L001_R1_001.fastq.gz FliTp124hpf_S27_L001_R2_001.fastq.gz", "fastq fastq", 261098334.0, 2072209.0, "E MTAB 13196:FliTp124hpf S27 L001", "0:28 1:98", "A:76098436;C:58031830;G:57099955;T:69729759;N:138354", 28, 98, null, null, 76098436, 58031830, 57099955, 69729759, 138354, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00109, 0.87641, 0.00062, 0.0976, 0.99837, 0.90065, 0.45555, 0.48712, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11755, "ERR11758589", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S16_L005_R1_001.fastq.gz FliTp124hpf_S16_L005_R2_001.fastq.gz", "fastq fastq", 1168367130.0, 9272755.0, "E MTAB 13196:FliTp124hpf S16 L005", "0:28 1:98", "A:323651598;C:269884286;G:268030176;T:306695030;N:106040", 28, 98, null, null, 323651598, 269884286, 268030176, 306695030, 106040, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00491, 0.90853, 0.00131, 0.07851, 0.99019, 0.84331, 0.41536, 0.48076, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11756, "ERR11758638", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S22_L001_R1_001.fastq.gz FliTp124hpf_S22_L001_R2_001.fastq.gz", "fastq fastq", 864786636.0, 6863386.0, "E MTAB 13196:FliTp124hpf S22 L001", "0:28 1:98", "A:241767760;C:198370882;G:198049093;T:226508751;N:90150", 28, 98, null, null, 241767760, 198370882, 198049093, 226508751, 90150, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00375, 0.89002, 0.00114, 0.0769, 0.99237, 0.84563, 0.41796, 0.48995, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11757, "ERR11758599", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S15_L005_R1_001.fastq.gz FliTp124hpf_S15_L005_R2_001.fastq.gz", "fastq fastq", 1795799502.0, 14252377.0, "E MTAB 13196:FliTp124hpf S15 L005", "0:28 1:98", "A:500590460;C:413239086;G:410401125;T:471402890;N:165941", 28, 98, null, null, 500590460, 413239086, 410401125, 471402890, 165941, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00492, 0.91242, 0.0012, 0.08044, 0.99007, 0.84668, 0.42778, 0.49291, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11758, "ERR11758601", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S26_L001_R1_001.fastq.gz FliTp124hpf_S26_L001_R2_001.fastq.gz", "fastq fastq", 266141358.0, 2112233.0, "E MTAB 13196:FliTp124hpf S26 L001", "0:28 1:98", "A:76996100;C:59592346;G:58963461;T:70457732;N:131719", 28, 98, null, null, 76996100, 59592346, 58963461, 70457732, 131719, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00106, 0.88422, 0.00046, 0.09358, 0.99782, 0.89449, 0.47826, 0.48948, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11759, "ERR11758630", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S14_L005_R1_001.fastq.gz FliTp124hpf_S14_L005_R2_001.fastq.gz", "fastq fastq", 1812847428.0, 14387678.0, "E MTAB 13196:FliTp124hpf S14 L005", "0:28 1:98", "A:502956890;C:417865079;G:416595454;T:475266679;N:163326", 28, 98, null, null, 502956890, 417865079, 416595454, 475266679, 163326, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00483, 0.91317, 0.00123, 0.07918, 0.99036, 0.84143, 0.40704, 0.4819, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11760, "ERR11758603", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S13_L005_R1_001.fastq.gz FliTp124hpf_S13_L005_R2_001.fastq.gz", "fastq fastq", 1544281830.0, 12256205.0, "E MTAB 13196:FliTp124hpf S13 L005", "0:28 1:98", "A:428008915;C:356252081;G:354333187;T:405545992;N:141655", 28, 98, null, null, 428008915, 356252081, 354333187, 405545992, 141655, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00507, 0.91025, 0.00138, 0.07858, 0.98987, 0.84295, 0.41793, 0.4891, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11761, "ERR11758613", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S21_L001_R1_001.fastq.gz FliTp124hpf_S21_L001_R2_001.fastq.gz", "fastq fastq", 761441436.0, 6043186.0, "E MTAB 13196:FliTp124hpf S21 L001", "0:28 1:98", "A:212876877;C:174700212;G:174244892;T:199537401;N:82054", 28, 98, null, null, 212876877, 174700212, 174244892, 199537401, 82054, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00334, 0.88899, 0.00106, 0.07762, 0.99322, 0.84476, 0.42792, 0.48783, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11762, "ERR11758645", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S23_L001_R1_001.fastq.gz FliTp124hpf_S23_L001_R2_001.fastq.gz", "fastq fastq", 873938772.0, 6936022.0, "E MTAB 13196:FliTp124hpf S23 L001", "0:28 1:98", "A:245075115;C:199879929;G:199312177;T:229576663;N:94888", 28, 98, null, null, 245075115, 199879929, 199312177, 229576663, 94888, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00361, 0.88671, 0.00104, 0.07855, 0.99255, 0.84723, 0.41141, 0.4885, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11763, "ERR11758598", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S28_L001_R1_001.fastq.gz FliTp124hpf_S28_L001_R2_001.fastq.gz", "fastq fastq", 164465532.0, 1305282.0, "E MTAB 13196:FliTp124hpf S28 L001", "0:28 1:98", "A:47319366;C:37063279;G:36394680;T:43602586;N:85621", 28, 98, null, null, 47319366, 37063279, 36394680, 43602586, 85621, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00117, 0.88222, 0.00058, 0.09358, 0.99799, 0.89217, 0.54867, 0.48545, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11764, "ERR11758593", "ERX11157721", "ERS16172939", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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.", "fli1tp1 24hpf", "SAMEA114192246", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP", 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:fli1tp1 24hpf p", "fli1tp1 24hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "FliTp124hpf_S24_L001_R1_001.fastq.gz FliTp124hpf_S24_L001_R2_001.fastq.gz", "fastq fastq", 558365976.0, 4431476.0, "E MTAB 13196:FliTp124hpf S24 L001", "0:28 1:98", "A:156054630;C:128109738;G:127885708;T:146256146;N:59754", 28, 98, null, null, 156054630, 128109738, 127885708, 146256146, 59754, "ERX11157721", "ERS16172939", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00345, 0.8879, 0.00104, 0.07718, 0.99322, 0.84364, 0.38266, 0.49193, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11765, "ERR11758635", "ERX11157720", "ERS16172938", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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 wt 22hpf", "SAMEA114192245", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede", 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 wt 22hpf p", "etv2 wt 22hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "Etv2Kaede_WT_S6_L001_R1_001.fastq.gz Etv2Kaede_WT_S6_L001_R2_001.fastq.gz", "fastq fastq", 1144014102.0, 9079477.0, "E MTAB 13196:Etv2Kaede WT S6 L001", "0:28 1:98", "A:316366230;C:260322813;G:259447166;T:307680623;N:197270", 28, 98, null, null, 316366230, 260322813, 259447166, 307680623, 197270, "ERX11157720", "ERS16172938", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00336, 0.89267, 0.00137, 0.13734, 0.99545, 0.81957, 0.3734, 0.53458, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11766, "ERR11758622", "ERX11157720", "ERS16172938", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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 wt 22hpf", "SAMEA114192245", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede", 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 wt 22hpf p", "etv2 wt 22hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "Etv2Kaede_WT_S8_L001_R2_001.fastq.gz Etv2Kaede_WT_S8_L001_R1_001.fastq.gz", "fastq fastq", 919270926.0, 7295801.0, "E MTAB 13196:Etv2Kaede WT S8 L001", "0:28 1:98", "A:259787542;C:207541571;G:206711907;T:245072713;N:157193", 28, 98, null, null, 259787542, 207541571, 206711907, 245072713, 157193, "ERX11157720", "ERS16172938", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00358, 0.88757, 0.00137, 0.15368, 0.99551, 0.83378, 0.36405, 0.53733, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11767, "ERR11758644", "ERX11157720", "ERS16172938", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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 wt 22hpf", "SAMEA114192245", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede", 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 wt 22hpf p", "etv2 wt 22hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "Etv2Kaede_WT_S5_L001_R2_001.fastq.gz Etv2Kaede_WT_S5_L001_R1_001.fastq.gz", "fastq fastq", 877658166.0, 6965541.0, "E MTAB 13196:Etv2Kaede WT S5 L001", "0:28 1:98", "A:243057461;C:199464116;G:198654377;T:236322700;N:159512", 28, 98, null, null, 243057461, 199464116, 198654377, 236322700, 159512, "ERX11157720", "ERS16172938", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00328, 0.88916, 0.00127, 0.13782, 0.99559, 0.81925, 0.38227, 0.53623, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11768, "ERR11758628", "ERX11157720", "ERS16172938", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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 wt 22hpf", "SAMEA114192245", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede", 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 wt 22hpf p", "etv2 wt 22hpf p", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 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", "Etv2Kaede_WT_S7_L001_R1_001.fastq.gz Etv2Kaede_WT_S7_L001_R2_001.fastq.gz", "fastq fastq", 930443598.0, 7384473.0, "E MTAB 13196:Etv2Kaede WT S7 L001", "0:28 1:98", "A:258539610;C:211017108;G:209074684;T:251641766;N:170430", 28, 98, null, null, 258539610, 211017108, 209074684, 251641766, 170430, "ERX11157720", "ERS16172938", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00355, 0.88938, 0.00148, 0.14297, 0.99569, 0.83358, 0.35626, 0.53314, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11769, "ERR11758631", "ERX11157719", "ERS16172937", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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_S10_L001_R2_001.fastq.gz Etv2_Traver_S10_L001_R1_001.fastq.gz", "fastq fastq", 1947733326.0, 15458201.0, "E MTAB 13196:Etv2 Traver S10 L001", "0:28 1:98", "A:532150077;C:434208725;G:472140578;T:508906834;N:327112", 28, 98, null, null, 532150077, 434208725, 472140578, 508906834, 327112, "ERX11157719", "ERS16172937", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00677, 0.92596, 0.00142, 0.07895, 0.98526, 0.85123, 0.42802, 0.53518, 28, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11770, "ERR11758646", "ERX11157719", "ERS16172937", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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_S28_L001_R2_001.fastq.gz Etv2_Traver_S28_L001_R1_001.fastq.gz", "fastq fastq", 1091426920.0, 8801830.0, "E MTAB 13196:Etv2 Traver S28 L001", "0:26 1:98", "A:302665480;C:247712584;G:269795015;T:271081940;N:171901", 26, 98, null, null, 302665480, 247712584, 269795015, 271081940, 171901, "ERX11157719", "ERS16172937", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00585, 0.90012, 0.00149, 0.07225, 0.98746, 0.84916, 0.39007, 0.54873, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11771, "ERR11758602", "ERX11157719", "ERS16172937", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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_S25_L001_R2_001.fastq.gz Etv2_Traver_S25_L001_R1_001.fastq.gz", "fastq fastq", 983616732.0, 7932393.0, "E MTAB 13196:Etv2 Traver S25 L001", "0:26 1:98", "A:272974243;C:222949925;G:242884450;T:244652916;N:155198", 26, 98, null, null, 272974243, 222949925, 242884450, 244652916, 155198, "ERX11157719", "ERS16172937", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00571, 0.90139, 0.00143, 0.07484, 0.98756, 0.85019, 0.40119, 0.54977, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11772, "ERR11758647", "ERX11157719", "ERS16172937", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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_S27_L001_R2_001.fastq.gz Etv2_Traver_S27_L001_R1_001.fastq.gz", "fastq fastq", 1162223232.0, 9372768.0, "E MTAB 13196:Etv2 Traver S27 L001", "0:26 1:98", "A:322910431;C:262934167;G:286614718;T:289578468;N:185448", 26, 98, null, null, 322910431, 262934167, 286614718, 289578468, 185448, "ERX11157719", "ERS16172937", "ERA25628220", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 2, 0.00563, 0.89924, 0.00128, 0.07464, 0.98762, 0.85064, 0.38525, 0.53889, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2023-08-01", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11773, "ERR11758634", "ERX11157719", "ERS16172937", "ERP149744", "PRJEB64563", "Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos", "E-MTAB-13196", "Transcriptome Analysis", "Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.", "ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01", 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"], [11777, "ERR11758595", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S36_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S36_L001_R1_001.fastq.gz", "fastq fastq", 211593816.0, 1679316.0, "E MTAB 13196:drl h2b dendra tb S36 L001", "0:28 1:98", "A:62689430;C:45809168;G:45709128;T:57272091;N:113999", 28, 98, null, null, 62689430, 45809168, 45709128, 57272091, 113999, "ERX11157718", "ERS16172936", "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, 0.00192, 0.91331, 0.00072, 0.14588, 0.99675, 0.89292, 0.51304, 0.63144, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11778, "ERR11758629", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S37_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S37_L001_R1_001.fastq.gz", "fastq fastq", 980164836.0, 7779086.0, "E MTAB 13196:drl h2b dendra tb S37 L001", "0:28 1:98", "A:281375011;C:216067640;G:222839674;T:259781180;N:101331", 28, 98, null, null, 281375011, 216067640, 222839674, 259781180, 101331, "ERX11157718", "ERS16172936", "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, 0.00817, 0.89718, 0.00237, 0.12153, 0.98912, 0.82643, 0.46403, 0.64954, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11779, "ERR11758618", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S39_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S39_L001_R1_001.fastq.gz", "fastq fastq", 12118302.0, 96177.0, "E MTAB 13196:drl h2b dendra tb S39 L001", "0:28 1:98", "A:3543790;C:2662872;G:2728134;T:3182383;N:1123", 28, 98, null, null, 3543790, 2662872, 2728134, 3182383, 1123, "ERX11157718", "ERS16172936", "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, 0.00786, 0.88963, 0.0025, 0.12543, 0.99403, 0.88635, 0.50098, 0.64694, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11780, "ERR11758643", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S5_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S5_L005_R1_001.fastq.gz", "fastq fastq", 2061022698.0, 16357323.0, "E MTAB 13196:drl h2b dendra tb S5 L005", "0:28 1:98", "A:587730953;C:457631700;G:470283474;T:545196979;N:179592", 28, 98, null, null, 587730953, 457631700, 470283474, 545196979, 179592, "ERX11157718", "ERS16172936", "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, 0.01192, 0.91661, 0.00336, 0.12397, 0.98518, 0.82568, 0.45692, 0.65555, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11781, "ERR11758610", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S38_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S38_L001_R1_001.fastq.gz", "fastq fastq", 924603120.0, 7338120.0, "E MTAB 13196:drl h2b dendra tb S38 L001", "0:28 1:98", "A:265987815;C:203824483;G:210024160;T:244670646;N:96016", 28, 98, null, null, 265987815, 203824483, 210024160, 244670646, 96016, "ERX11157718", "ERS16172936", "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, 0.00773, 0.89881, 0.00242, 0.12145, 0.98944, 0.82948, 0.50529, 0.66568, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11782, "ERR11758641", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S6_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S6_L005_R1_001.fastq.gz", "fastq fastq", 1954661562.0, 15513187.0, "E MTAB 13196:drl h2b dendra tb S6 L005", "0:28 1:98", "A:558769608;C:433724557;G:445550100;T:516443984;N:173313", 28, 98, null, null, 558769608, 433724557, 445550100, 516443984, 173313, "ERX11157718", "ERS16172936", "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, 0.0125, 0.91697, 0.00373, 0.12359, 0.98447, 0.82558, 0.4881, 0.6456, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11783, "ERR11758591", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S35_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S35_L001_R1_001.fastq.gz", "fastq fastq", 4717188.0, 37438.0, "E MTAB 13196:drl h2b dendra tb S35 L001", "0:28 1:98", "A:1419430;C:1014265;G:1016661;T:1264642;N:2190", 28, 98, null, null, 1419430, 1014265, 1016661, 1264642, 2190, "ERX11157718", "ERS16172936", "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, 0.0012, 0.65482, 0.00054, 0.10783, 0.99953, 0.97157, 0.625, 0.63689, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11784, "ERR11758606", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S34_L001_R1_001.fastq.gz drl_h2b-dendra_tb_S34_L001_R2_001.fastq.gz", "fastq fastq", 303645636.0, 2409886.0, "E MTAB 13196:drl h2b dendra tb S34 L001", "0:28 1:98", "A:90748559;C:65369482;G:65969002;T:81405258;N:153335", 28, 98, null, null, 90748559, 65369482, 65969002, 81405258, 153335, "ERX11157718", "ERS16172936", "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, 0.00228, 0.91262, 0.00099, 0.14666, 0.99638, 0.89006, 0.47177, 0.63109, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11785, "ERR11758640", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S40_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S40_L001_R1_001.fastq.gz", "fastq fastq", 661361022.0, 5248897.0, "E MTAB 13196:drl h2b dendra tb S40 L001", "0:28 1:98", "A:190087869;C:145985661;G:150124621;T:175095762;N:67109", 28, 98, null, null, 190087869, 145985661, 150124621, 175095762, 67109, "ERX11157718", "ERS16172936", "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, 0.00785, 0.89784, 0.00251, 0.12159, 0.98948, 0.83055, 0.46095, 0.64951, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11786, "ERR11758605", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S7_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S7_L005_R1_001.fastq.gz", "fastq fastq", 25157790.0, 199665.0, "E MTAB 13196:drl h2b dendra tb S7 L005", "0:28 1:98", "A:7330053;C:5600451;G:5635840;T:6589498;N:1948", 28, 98, null, null, 7330053, 5600451, 5635840, 6589498, 1948, "ERX11157718", "ERS16172936", "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, 0.01201, 0.91385, 0.00341, 0.12826, 0.98595, 0.85161, 0.49226, 0.64953, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11787, "ERR11758600", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S8_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S8_L005_R1_001.fastq.gz", "fastq fastq", 1422735804.0, 11291554.0, "E MTAB 13196:drl h2b dendra tb S8 L005", "0:28 1:98", "A:405788442;C:317299433;G:322206476;T:377317416;N:124037", 28, 98, null, null, 405788442, 317299433, 322206476, 377317416, 124037, "ERX11157718", "ERS16172936", "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, 0.01226, 0.91547, 0.0037, 0.12565, 0.9849, 0.83662, 0.48279, 0.64531, 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", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [11788, "ERR11758616", "ERX11157718", "ERS16172936", "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 tb", "SAMEA114192243", "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:SAMEA114192243|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 tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent 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 tb|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 tb p", "drl tb 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_tb_S33_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S33_L001_R1_001.fastq.gz", "fastq fastq", 328918212.0, 2610462.0, "E MTAB 13196:drl h2b dendra tb S33 L001", "0:28 1:98", "A:98036464;C:71090137;G:71650807;T:87969481;N:171323", 28, 98, null, null, 98036464, 71090137, 71650807, 87969481, 171323, "ERX11157718", "ERS16172936", "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, 0.00197, 0.89969, 0.00087, 0.14269, 0.99681, 0.89134, 0.49763, 0.63651, 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", "Undetermined", "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"], [15009, "ERR12306826", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L003_I1_001.fastq.gz 230324-Coated_S1_L003_I2_001.fastq.gz 230324-Coated_S1_L003_R1_001.fastq.gz 230324-Coated_S1_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 10050750400.0, 62817190.0, "E MTAB 13554:230324 Coated S1 L003", "0:10 1:10 2:30 3:110", "A:1894211982;C:1556769050;G:1595134885;T:1863244619;N:530364", 10, 10, 30, 110, 1894211982, 1556769050, 1595134885, 1863244619, 530364, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 1909, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", 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