{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"PolyA\", experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and tissue_curation_coarse = \"All anatomical structures\"", "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. Libraries were constructed using the 10x v2 chemistry.", "Sample 2", "SAMEA6873729", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873729|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 2|scientific name:Danio rerio|sex:mixed", 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 2 s", "Sample 2 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\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:8|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", "cDNA8h_1_S2_L001.bam", "bam", 10087287534.0, 99874134.0, "E MTAB 9193:cDNA8h 1 S2 L001", "0:101", "A:2892833391;C:2022466595;G:2198646699;T:2962268446;N:11072403", 101, null, null, null, 2892833391, 2022466595, 2198646699, 2962268446, 11072403, "ERX4155254", "ERS4601292", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93609, null, 0.12902, null, 0.82158, null, 0.5062, 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"], [9899, "ERR4194115", "ERX4155254", "ERS4601292", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", 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 2", "SAMEA6873729", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada", "ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873729|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 2|scientific name:Danio rerio|sex:mixed", 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 2 s", "Sample 2 s", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200\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:8|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", "cDNA8h_1_S2_L002.bam", "bam", 10191911414.0, 100910014.0, "E MTAB 9193:cDNA8h 1 S2 L002", "0:101", "A:2923216190;C:2043975715;G:2221734566;T:2992798366;N:10186577", 101, null, null, null, 2923216190, 2043975715, 2221734566, 2992798366, 10186577, "ERX4155254", "ERS4601292", "ERA2667966", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", "Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive", 1, 0.93445, null, 0.13038, null, 0.824, null, 0.49774, 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"], [9900, "ERR4194112", "ERX4155253", "ERS4601291", "ERP122151", "PRJEB38705", "Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish", "E-MTAB-9193", "Transcriptome Analysis", "TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", 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_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"], [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"], [15010, "ERR12306829", "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_L004_I1_001.fastq.gz 230324-Coated_S1_L004_I2_001.fastq.gz 230324-Coated_S1_L004_R1_001.fastq.gz 230324-Coated_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 9780757760.0, 61129736.0, "E MTAB 13554:230324 Coated S1 L004", "0:10 1:10 2:30 3:110", "A:1844808667;C:1516149264;G:1549838165;T:1813091860;N:383004", 10, 10, 30, 110, 1844808667, 1516149264, 1549838165, 1813091860, 383004, "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"], [15011, "ERR12306828", "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_L002_I1_001.fastq.gz 230324-Coated_S1_L002_I2_001.fastq.gz 230324-Coated_S1_L002_R1_001.fastq.gz 230324-Coated_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 9639368480.0, 60246053.0, "E MTAB 13554:230324 Coated S1 L002", "0:10 1:10 2:30 3:110", "A:1817388578;C:1494319441;G:1527564319;T:1787447672;N:345820", 10, 10, 30, 110, 1817388578, 1494319441, 1527564319, 1787447672, 345820, "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"], [15012, "ERR12306832", "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_L001_I1_001.fastq.gz 230324-Coated_S1_L001_I2_001.fastq.gz 230324-Coated_S1_L001_R1_001.fastq.gz 230324-Coated_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 9823147840.0, 61394674.0, "E MTAB 13554:230324 Coated S1 L001", "0:10 1:10 2:30 3:110", "A:1851113558;C:1521671335;G:1558230628;T:1822067428;N:331191", 10, 10, 30, 110, 1851113558, 1521671335, 1558230628, 1822067428, 331191, "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"], [15013, "ERR12306833", "ERX11683774", "ERS17043894", "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.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|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:Uncoated|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:Uncoated p", "Uncoated 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-Uncoated_S2_L001_I1_001.fastq.gz 230324-Uncoated_S2_L001_I2_001.fastq.gz 230324-Uncoated_S2_L001_R1_001.fastq.gz 230324-Uncoated_S2_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 8871716800.0, 55448230.0, "E MTAB 13554:230324 Uncoated S2 L001", "0:10 1:10 2:30 3:110", "A:1718985845;C:1319560520;G:1372197713;T:1688254655;N:306567", 10, 10, 30, 110, 1718985845, 1319560520, 1372197713, 1688254655, 306567, "ERX11683774", "ERS17043894", "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"], [15014, "ERR12306830", "ERX11683774", "ERS17043894", "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.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|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:Uncoated|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:Uncoated p", "Uncoated 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-Uncoated_S2_L003_I1_001.fastq.gz 230324-Uncoated_S2_L003_I2_001.fastq.gz 230324-Uncoated_S2_L003_R1_001.fastq.gz 230324-Uncoated_S2_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 9075478720.0, 56721742.0, "E MTAB 13554:230324 Uncoated S2 L003", "0:10 1:10 2:30 3:110", "A:1758677834;C:1349774831;G:1404463433;T:1725994897;N:480625", 10, 10, 30, 110, 1758677834, 1349774831, 1404463433, 1725994897, 480625, "ERX11683774", "ERS17043894", "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"], [15015, "ERR12306831", "ERX11683774", "ERS17043894", "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.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|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:Uncoated|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:Uncoated p", "Uncoated 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-Uncoated_S2_L002_I1_001.fastq.gz 230324-Uncoated_S2_L002_I2_001.fastq.gz 230324-Uncoated_S2_L002_R1_001.fastq.gz 230324-Uncoated_S2_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 8705210880.0, 54407568.0, "E MTAB 13554:230324 Uncoated S2 L002", "0:10 1:10 2:30 3:110", "A:1687330583;C:1295837902;G:1345522657;T:1655826422;N:314916", 10, 10, 30, 110, 1687330583, 1295837902, 1345522657, 1655826422, 314916, "ERX11683774", "ERS17043894", "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"], [15016, "ERR12306827", "ERX11683774", "ERS17043894", "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.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|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:Uncoated|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:Uncoated p", "Uncoated 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-Uncoated_S2_L004_I1_001.fastq.gz 230324-Uncoated_S2_L004_I2_001.fastq.gz 230324-Uncoated_S2_L004_R1_001.fastq.gz 230324-Uncoated_S2_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 8846203360.0, 55288771.0, "E MTAB 13554:230324 Uncoated S2 L004", "0:10 1:10 2:30 3:110", "A:1715100047;C:1316853239;G:1367208350;T:1682248092;N:355082", 10, 10, 30, 110, 1715100047, 1316853239, 1367208350, 1682248092, 355082, "ERX11683774", "ERS17043894", "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": 28, "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", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_selection\" = :p0 and \"experiment.library_source\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "PolyA", "p1": "TRANSCRIPTOMIC SINGLE CELL", "p2": "All anatomical structures"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&tissue_curation_coarse=All+anatomical+structures", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "PolyA", "label": "PolyA", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "Embryo", "label": "Embryo", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&devstage_curation=Multi-stage", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&devstage_curation=Hatching", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Whole Organism", "label": "Whole Organism", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&tissue_curation=Whole+Organism", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "10x", "label": "10x", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures&technology=10x", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 73.8934950059047}