{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[9892, "ERR4172795", "ERX4136409", "ERS4580819", "ERP121885", "PRJEB38455", "RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E-MTAB-9113", "Transcriptome Analysis", "RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22", null, "Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion", "sibling 3", "SAMEA6853229", "Centre for Developmental Neurobiology King's College London", "ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853229|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing; 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Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.", "ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01", null, "Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 \u03bcl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 \u03bcm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. 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Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. 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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"], [25182, "SRR25670729", "SRX21396042", "SRS18636200", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA germ ring PAL seq v4", "GSM7716871", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA germ ring PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716871", "GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER", "GSM7716871 r1", "GSM7716871", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read2.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read1.fastq.gz", "fastq fastq", 2834842912.0, 9234016.0, "GSM7716871 r1", "0:52 1:255", "A:725811118;C:702410592;G:747583409;T:651018348;N:8019445", 52, 255, null, null, 725811118, 702410592, 747583409, 651018348, 8019445, "SRX21396042", "SRS18636200", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00023, 0.30494, 8e-05, 0.01793, 0.99967, 0.99971, 0.5, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25183, "SRR25670730", "SRX21396042", "SRS18636200", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA germ ring PAL seq v4", "GSM7716871", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA germ ring PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716871", "GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER", "GSM7716871 r1", "GSM7716871", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3473033898.0, 11312814.0, "GSM7716871 r2", "0:52 1:255", "A:853178471;C:899976159;G:962100712;T:750811461;N:6967095", 52, 255, null, null, 853178471, 899976159, 962100712, 750811461, 6967095, "SRX21396042", "SRS18636200", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00049, 0.0, 0.00012, 0.0, 0.99941, 1.0, 0.64864, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25184, "SRR25670731", "SRX21396041", "SRS18636199", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA zfs:0000015 PAL seq v4", "GSM7716870", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA zfs:0000015 PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716870", "GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER", "GSM7716870 r1", "GSM7716870", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2695203962.0, 8779166.0, "GSM7716870 r1", "0:52 1:255", "A:684535386;C:669852151;G:719008886;T:614209811;N:7597728", 52, 255, null, null, 684535386, 669852151, 719008886, 614209811, 7597728, "SRX21396041", "SRS18636199", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00117, 0.35837, 0.00017, 0.00682, 0.99859, 0.99963, 0.69473, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25185, "SRR25670732", "SRX21396041", "SRS18636199", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA zfs:0000015 PAL seq v4", "GSM7716870", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA zfs:0000015 PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716870", "GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER", "GSM7716870 r1", "GSM7716870", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read2.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read1.fastq.gz", "fastq fastq", 3476338446.0, 11323578.0, "GSM7716870 r2", "0:52 1:255", "A:841832234;C:898325199;G:968774318;T:760398070;N:7008625", 52, 255, null, null, 841832234, 898325199, 968774318, 760398070, 7008625, "SRX21396041", "SRS18636199", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00245, 0.0, 0.00047, 0.0, 0.99803, 1.0, 0.58536, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25186, "SRR25670733", "SRX21396040", "SRS18636198", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA sphere PAL seq v4", "GSM7716869", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA sphere PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716869", "GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER", "GSM7716869 r1", "GSM7716869", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 3211687254.0, 10461522.0, "GSM7716869 r1", "0:52 1:255", "A:813560400;C:775326762;G:854563477;T:759161458;N:9075157", 52, 255, null, null, 813560400, 775326762, 854563477, 759161458, 9075157, "SRX21396040", "SRS18636198", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00088, 0.43191, 0.0004, 0.01556, 0.99916, 0.99961, 0.55769, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25187, "SRR25670734", "SRX21396040", "SRS18636198", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA sphere PAL seq v4", "GSM7716869", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA sphere PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716869", "GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER", "GSM7716869 r1", "GSM7716869", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3179916131.0, 10358033.0, "GSM7716869 r2", "0:52 1:255", "A:771755667;C:804256300;G:883166175;T:714242073;N:6495916", 52, 255, null, null, 771755667, 804256300, 883166175, 714242073, 6495916, "SRX21396040", "SRS18636198", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00186, 0.0, 0.00088, 0.0, 0.99862, 1.0, 0.64705, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25190, "SRR25670737", "SRX21396038", "SRS18636196", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA 128cell PAL seq v4", "GSM7716867", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 128cell PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716867", "GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER", "GSM7716867 r1", "GSM7716867", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2104868443.0, 6856249.0, "GSM7716867 r1", "0:52 1:255", "A:539122676;C:505234642;G:558793048;T:495876292;N:5841785", 52, 255, null, null, 539122676, 505234642, 558793048, 495876292, 5841785, "SRX21396038", "SRS18636196", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00035, 0.29379, 7e-05, 0.01129, 0.99949, 0.99971, 0.55882, 0.79591, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25191, "SRR25670738", "SRX21396038", "SRS18636196", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA 128cell PAL seq v4", "GSM7716867", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 128cell PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716867", "GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER", "GSM7716867 r1", "GSM7716867", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3135806371.0, 10214353.0, "GSM7716867 r2", "0:52 1:255", "A:776612486;C:774126305;G:853951502;T:724788612;N:6327466", 52, 255, null, null, 776612486, 774126305, 853951502, 724788612, 6327466, "SRX21396038", "SRS18636196", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00066, 0.0, 0.00011, 0.0, 0.99939, 1.0, 0.55737, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25192, "SRR25670739", "SRX21396037", "SRS18636195", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA 8cell PAL seq v4", "GSM7716866", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 8cell PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716866", "GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER", "GSM7716866 r1", "GSM7716866", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2618998887.0, 8530941.0, "GSM7716866 r1", "0:52 1:255", "A:673066508;C:641446717;G:706546263;T:590452494;N:7486905", 52, 255, null, null, 673066508, 641446717, 706546263, 590452494, 7486905, "SRX21396037", "SRS18636195", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.0009, 0.43244, 0.00014, 0.0054, 0.99902, 0.99967, 0.54901, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25193, "SRR25670740", "SRX21396037", "SRS18636195", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.", null, null, null, "Fish embryo mRNA 8cell PAL seq v4", "GSM7716866", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 8cell PAL seq v4", "For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters \u201c runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716866", "GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER", "GSM7716866 r1", "GSM7716866", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 \u00b5g/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5 0.5 mM EDTA 1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined precipitated with ethanol and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330 50 mM HEPES pH 7.5 10 mM MgCl2 10 mM dithiothreitol 1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation RNA was extracted with phenol/chloroform precipitated with ethanol and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l incubated at 65\u00b0C for 5 min and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer 500 \u00b5M dNTPs 5 mM dithiothreitol 1 unit/\u00b5l SUPERase\u2022In and 200 units SuperScript III Thermo Fisher 18080044 at 50\u00b0C for 1 hr. post reverse transcription RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos fish embryos and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation and polyA selected mRNA from HeLa cells was used as spike in replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined precipitated with ethanol and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3028839589.0, 9865927.0, "GSM7716866 r2", "0:52 1:255", "A:756368817;C:758868409;G:836949742;T:670545278;N:6107343", 52, 255, null, null, 756368817, 758868409, 836949742, 670545278, 6107343, "SRX21396037", "SRS18636195", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00156, 0.0, 0.00026, 0.0, 0.99835, 1.0, 0.44791, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25277, "SRR30160454", "SRX25627658", "SRS22272474", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT bud 10 hpf charged tRNA seqrep 3", "GSM8441306", null, "tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing", "WT bud 10 hpf charged tRNA seqrep 3", "Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions", "10 hpf embryos", null, "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "cell type:10 hpf embryos", "GSM8441306", "GSM8441306: WT bud 10 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq", "GSM8441306 r1", "GSM8441306", "1", "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457111", null, null, "10hpf_aa_rep3.fastq.gz", "fastq", 193965330.0, 3367323.0, "GSM8441306 r1", "0:57.60", "A:36799299;C:55100074;G:53758955;T:48306966;N:36", 57, null, null, null, 36799299, 55100074, 53758955, 48306966, 36, "SRX25627658", "SRS22272474", "SRA1941998", "Max Planck Institute of Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.34405, null, 0.05049, null, 0.89471, null, 0.46469, null, 88, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-08-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25278, "SRR30160455", "SRX25627657", "SRS22272473", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT bud 10 hpf charged tRNA seqrep 2", "GSM8441305", null, "tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing", "WT bud 10 hpf charged tRNA seqrep 2", "Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions", "10 hpf embryos", null, "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "cell type:10 hpf embryos", "GSM8441305", "GSM8441305: WT bud 10 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq", "GSM8441305 r1", "GSM8441305", "1", "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457111", null, null, "10hpf_aa_rep2.fastq.gz", "fastq", 138524715.0, 2369009.0, "GSM8441305 r1", "0:58.47", "A:26396279;C:39139297;G:38459048;T:34530060;N:31", 58, null, null, null, 26396279, 39139297, 38459048, 34530060, 31, "SRX25627657", "SRS22272473", "SRA1941998", "Max Planck Institute of Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.35458, null, 0.05179, null, 0.89424, null, 0.46401, null, 74, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-08-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25279, "SRR30160456", "SRX25627656", "SRS22272472", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT bud 10 hpf charged tRNA seqrep 1", "GSM8441304", null, "tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing", "WT bud 10 hpf charged tRNA seqrep 1", "Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions", "10 hpf embryos", null, "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "cell type:10 hpf embryos", "GSM8441304", "GSM8441304: WT bud 10 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq", "GSM8441304 r1", "GSM8441304", "1", "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457111", null, null, "10hpf_aa_rep1.fastq.gz", "fastq", 54473618.0, 946419.0, "GSM8441304 r1", "0:57.56", "A:10345022;C:15413782;G:15135500;T:13579304;N:10", 57, null, null, null, 10345022, 15413782, 15135500, 13579304, 10, "SRX25627656", "SRS22272472", "SRA1941998", "Max Planck Institute of Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.36103, null, 0.0515, null, 0.89227, null, 0.4748, null, 81, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-08-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25280, "SRR30160457", "SRX25627655", "SRS22272471", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf charged tRNA seqrep 3", "GSM8441303", null, "tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing", "WT sphere 4 hpf charged tRNA seqrep 3", "Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions", "4 hpf embryos", null, "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "cell type:4 hpf embryos", "GSM8441303", "GSM8441303: WT sphere 4 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq", "GSM8441303 r1", "GSM8441303", "1", "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457111", null, null, "4hpf_aa_rep3.fastq.gz", "fastq", 100810543.0, 1747597.0, "GSM8441303 r1", "0:57.69", "A:20466558;C:28054923;G:26849246;T:25439798;N:18", 57, null, null, null, 20466558, 28054923, 26849246, 25439798, 18, "SRX25627655", "SRS22272471", "SRA1941998", "Max Planck Institute of Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.36374, null, 0.06294, null, 0.87316, null, 0.54642, null, 39, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-08-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25281, "SRR30160458", "SRX25627654", "SRS22272470", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf charged tRNA seqrep 2", "GSM8441302", null, "tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing", "WT sphere 4 hpf charged tRNA seqrep 2", "Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions", "4 hpf embryos", null, "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "cell type:4 hpf embryos", "GSM8441302", "GSM8441302: WT sphere 4 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq", "GSM8441302 r1", "GSM8441302", "1", "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457111", null, null, "4hpf_aa_rep2.fastq.gz", "fastq", 121662759.0, 2046536.0, "GSM8441302 r1", "0:59.45", "A:24519095;C:33689156;G:32726095;T:30728382;N:31", 59, null, null, null, 24519095, 33689156, 32726095, 30728382, 31, "SRX25627654", "SRS22272470", "SRA1941998", "Max Planck Institute of Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.3726, null, 0.06263, null, 0.87136, null, 0.55584, null, 31, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-08-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25282, "SRR30160459", "SRX25627653", "SRS22272469", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf charged tRNA seqrep 1", "GSM8441301", null, "tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing", "WT sphere 4 hpf charged tRNA seqrep 1", "Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions", "4 hpf embryos", null, "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "cell type:4 hpf embryos", "GSM8441301", "GSM8441301: WT sphere 4 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq", "GSM8441301 r1", "GSM8441301", "1", "Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457111", null, null, "4hpf_aa_rep1.fastq.gz", "fastq", 124990980.0, 2116213.0, "GSM8441301 r1", "0:59.06", "A:25487542;C:34621140;G:33284460;T:31597816;N:22", 59, null, null, null, 25487542, 34621140, 33284460, 31597816, 22, "SRX25627653", "SRS22272469", "SRA1941998", "Max Planck Institute of Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.36013, null, 0.05967, null, 0.87387, null, 0.55002, null, 44, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-08-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31773, "SRR28590145", "SRX24189497", "SRS20963520", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "WT shield PGCs RNA rep2", "GSM8193374", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:Wile type|geo loc name:missing|collection date:missing", "WT shield PGCs RNA rep2", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 214 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:Wile type", "GSM8193374", "GSM8193374: WT shield PGCs RNA rep2; Danio rerio; RNA Seq", "GSM8193374 r1", "GSM8193374", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "WT_shield_PGCs_RNA_rep2_r1.fq.gz WT_shield_PGCs_RNA_rep2_r2.fq.gz", "fastq fastq", 1476298800.0, 4920996.0, "GSM8193374 r1", "0:150 1:150", "A:364072227;C:345274481;G:387289011;T:379660776;N:2305", 150, 150, null, null, 364072227, 345274481, 387289011, 379660776, 2305, "SRX24189497", "SRS20963520", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.9277, 0.92845, 0.26727, 0.2672, 0.86803, 0.86969, 0.75933, 0.75985, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31774, "SRR28590146", "SRX24189496", "SRS20963519", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "WT shield PGCs RNA rep1", "GSM8193373", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:Wile type|geo loc name:missing|collection date:missing", "WT shield PGCs RNA rep1", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 212 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:Wile type", "GSM8193373", "GSM8193373: WT shield PGCs RNA rep1; Danio rerio; RNA Seq", "GSM8193373 r1", "GSM8193373", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "WT_shield_PGCs_RNA_rep1_r2.fq.gz WT_shield_PGCs_RNA_rep1_r1.fq.gz", "fastq fastq", 2758778100.0, 9195927.0, "GSM8193373 r1", "0:150 1:150", "A:769058521;C:582931819;G:614181069;T:792602904;N:3787", 150, 150, null, null, 769058521, 582931819, 614181069, 792602904, 3787, "SRX24189496", "SRS20963519", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.93691, 0.91581, 0.06844, 0.06665, 0.7683, 0.76995, 0.53645, 0.52363, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31775, "SRR28590147", "SRX24189495", "SRS20963518", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "WT bud PGCs RNA rep2", "GSM8193372", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:Wile type|geo loc name:missing|collection date:missing", "WT bud PGCs RNA rep2", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 210 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:Wile type", "GSM8193372", "GSM8193372: WT bud PGCs RNA rep2; Danio rerio; RNA Seq", "GSM8193372 r1", "GSM8193372", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "WT_bud_PGCs_RNA_rep2_r1.fq.gz WT_bud_PGCs_RNA_rep2_r2.fq.gz", "fastq fastq", 3111261300.0, 10370871.0, "GSM8193372 r1", "0:150 1:150", "A:817262319;C:691724200;G:751270343;T:850999265;N:5173", 150, 150, null, null, 817262319, 691724200, 751270343, 850999265, 5173, "SRX24189495", "SRS20963518", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.90729, 0.9053, 0.11596, 0.1166, 0.79963, 0.79981, 0.60276, 0.59912, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31776, "SRR28590148", "SRX24189494", "SRS20963517", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "WT bud PGCs RNA rep1", "GSM8193371", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:Wile type|geo loc name:missing|collection date:missing", "WT bud PGCs RNA rep1", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 208 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:Wile type", "GSM8193371", "GSM8193371: WT bud PGCs RNA rep1; Danio rerio; RNA Seq", "GSM8193371 r1", "GSM8193371", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "WT_bud_PGCs_RNA_rep1_r1.fq.gz WT_bud_PGCs_RNA_rep1_r2.fq.gz", "fastq fastq", 3758269200.0, 12527564.0, "GSM8193371 r1", "0:150 1:150", "A:1041649283;C:801966468;G:845188264;T:1069459832;N:5353", 150, 150, null, null, 1041649283, 801966468, 845188264, 1069459832, 5353, "SRX24189494", "SRS20963517", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.93714, 0.91161, 0.07974, 0.07673, 0.75785, 0.76037, 0.52906, 0.52822, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31777, "SRR28590149", "SRX24189493", "SRS20963516", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "pigu homo shield PGCs RNA rep2", "GSM8193370", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo|geo loc name:missing|collection date:missing", "pigu homo shield PGCs RNA rep2", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 206 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo", "GSM8193370", "GSM8193370: pigu homo shield PGCs RNA rep2; Danio rerio; RNA Seq", "GSM8193370 r1", "GSM8193370", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "pigu_homo_shield_PGCs_RNA_rep2_r2.fq.gz pigu_homo_shield_PGCs_RNA_rep2_r1.fq.gz", "fastq fastq", 875630700.0, 2918769.0, "GSM8193370 r1", "0:150 1:150", "A:229625544;C:190227589;G:217096984;T:238679075;N:1508", 150, 150, null, null, 229625544, 190227589, 217096984, 238679075, 1508, "SRX24189493", "SRS20963516", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.81852, 0.81643, 0.19346, 0.19329, 0.89852, 0.89897, 0.83525, 0.83082, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31778, "SRR28590150", "SRX24189492", "SRS20963515", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "pigu homo shield PGCs RNA rep1", "GSM8193369", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo|geo loc name:missing|collection date:missing", "pigu homo shield PGCs RNA rep1", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 204 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo", "GSM8193369", "GSM8193369: pigu homo shield PGCs RNA rep1; Danio rerio; RNA Seq", "GSM8193369 r1", "GSM8193369", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "pigu_homo_shield_PGCs_RNA_rep1_r2.fq.gz pigu_homo_shield_PGCs_RNA_rep1_r1.fq.gz", "fastq fastq", 2204383800.0, 7347946.0, "GSM8193369 r1", "0:150 1:150", "A:618947181;C:459789570;G:491705141;T:633938869;N:3039", 150, 150, null, null, 618947181, 459789570, 491705141, 633938869, 3039, "SRX24189492", "SRS20963515", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.91971, 0.9203, 0.0732, 0.07256, 0.77512, 0.77516, 0.53347, 0.53419, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31779, "SRR28590151", "SRX24189491", "SRS20963514", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "pigu homo bud PGCs RNA rep2", "GSM8193368", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo|geo loc name:missing|collection date:missing", "pigu homo bud PGCs RNA rep2", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 202 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo", "GSM8193368", "GSM8193368: pigu homo bud PGCs RNA rep2; Danio rerio; RNA Seq", "GSM8193368 r1", "GSM8193368", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "pigu_homo_bud_PGCs_RNA_rep2_r1.fq.gz pigu_homo_bud_PGCs_RNA_rep2_r2.fq.gz", "fastq fastq", 2137638000.0, 7125460.0, "GSM8193368 r1", "0:150 1:150", "A:588045273;C:460739300;G:496293927;T:592556088;N:3412", 150, 150, null, null, 588045273, 460739300, 496293927, 592556088, 3412, "SRX24189491", "SRS20963514", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.36533, 0.36278, 0.05703, 0.057, 0.87754, 0.87811, 0.60206, 0.59677, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31780, "SRR28590152", "SRX24189490", "SRS20963513", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "pigu homo bud PGCs RNA rep1", "GSM8193367", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo|geo loc name:missing|collection date:missing", "pigu homo bud PGCs RNA rep1", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo", "GSM8193367", "GSM8193367: pigu homo bud PGCs RNA rep1; Danio rerio; RNA Seq", "GSM8193367 r1", "GSM8193367", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "pigu_homo_bud_PGCs_RNA_rep1_r1.fq.gz pigu_homo_bud_PGCs_RNA_rep1_r2.fq.gz", "fastq fastq", 2734187100.0, 9113957.0, "GSM8193367 r1", "0:150 1:150", "A:729072634;C:614811431;G:644751435;T:745548063;N:3537", 150, 150, null, null, 729072634, 614811431, 644751435, 745548063, 3537, "SRX24189490", "SRS20963513", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.94018, 0.93763, 0.11685, 0.1143, 0.77749, 0.78204, 0.50988, 0.50832, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33008, "SRR29632270", "SRX25138332", "SRS21830414", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.", null, null, null, "Bmp4 explant 24h", "GSM8366755", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 24h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 \u03bcg/ml gentamycin 100 \u03bcM 2 mercaptoethanol 1\u00d7 antibiotic antimycotic 10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366755", "GSM8366755: Bmp4 explant 24h; Danio rerio; RNA Seq", "GSM8366755 r1", "GSM8366755", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4_24h_S1_L001_R1_001.fastq.gz Bmp4_24h_S1_L001_R2_001.fastq.gz", "fastq fastq", 49098784294.0, 412594826.0, "GSM8366755 r1", "0:28 1:91", "A:13643133254;C:11126085942;G:11676909916;T:12651522663;N:1132519", 28, 91, null, null, 13643133254, 11126085942, 11676909916, 12651522663, 1132519, "SRX25138332", "SRS21830414", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33009, "SRR29632271", "SRX25138331", "SRS21830413", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.", null, null, null, "Bmp4 explant 18h", "GSM8366754", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 18h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 \u03bcg/ml gentamycin 100 \u03bcM 2 mercaptoethanol 1\u00d7 antibiotic antimycotic 10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366754", "GSM8366754: Bmp4 explant 18h; Danio rerio; RNA Seq", "GSM8366754 r1", "GSM8366754", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4_18h_S1_L001_R1_001.fastq.gz Bmp4_18h_S1_L001_R2_001.fastq.gz", "fastq fastq", 44863080801.0, 377000679.0, "GSM8366754 r1", "0:28 1:91", "A:12441486571;C:10199111519;G:10790306255;T:11430847129;N:1329327", 28, 91, null, null, 12441486571, 10199111519, 10790306255, 11430847129, 1329327, "SRX25138331", "SRS21830413", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33010, "SRR29632272", "SRX25138330", "SRS21830412", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.", null, null, null, "Bmp4 explant 12h", "GSM8366753", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 12h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 \u03bcg/ml gentamycin 100 \u03bcM 2 mercaptoethanol 1\u00d7 antibiotic antimycotic 10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366753", "GSM8366753: Bmp4 explant 12h; Danio rerio; RNA Seq", "GSM8366753 r1", "GSM8366753", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4_12h_S1_L001_R1_001.fastq.gz Bmp4_12h_S1_L001_R2_001.fastq.gz", "fastq fastq", 50138128747.0, 421328813.0, "GSM8366753 r1", "0:28 1:91", "A:14089229753;C:10936347905;G:11403388741;T:13708020723;N:1141625", 28, 91, null, null, 14089229753, 10936347905, 11403388741, 13708020723, 1141625, "SRX25138330", "SRS21830412", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33011, "SRR29632273", "SRX25138329", "SRS21830410", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.", null, null, null, "Bmp4 explant 10h", "GSM8366752", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 10h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 \u03bcg/ml gentamycin 100 \u03bcM 2 mercaptoethanol 1\u00d7 antibiotic antimycotic 10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366752", "GSM8366752: Bmp4 explant 10h; Danio rerio; RNA Seq", "GSM8366752 r1", "GSM8366752", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4-10h_S1_L001_R1_001.fastq.gz Bmp4-10h_S1_L001_R2_001.fastq.gz", "fastq fastq", 149164547700.0, 497215159.0, "GSM8366752 r1", "0:150 1:150", "A:44020073879;C:31344780625;G:29505876494;T:44289819189;N:3997513", 150, 150, null, null, 44020073879, 31344780625, 29505876494, 44289819189, 3997513, "SRX25138329", "SRS21830410", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33012, "SRR29632274", "SRX25138328", "SRS21830409", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.", null, null, null, "Bmp4 explant 8h", "GSM8366751", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 8h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 \u03bcg/ml gentamycin 100 \u03bcM 2 mercaptoethanol 1\u00d7 antibiotic antimycotic 10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366751", "GSM8366751: Bmp4 explant 8h; Danio rerio; RNA Seq", "GSM8366751 r1", "GSM8366751", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4-8h_S1_L001_R1_001.fastq.gz Bmp4-8h_S1_L001_R2_001.fastq.gz", "fastq fastq", 118709118600.0, 395697062.0, "GSM8366751 r1", "0:150 1:150", "A:35474636770;C:23305712896;G:22894585568;T:37031410017;N:2773349", 150, 150, null, null, 35474636770, 23305712896, 22894585568, 37031410017, 2773349, "SRX25138328", "SRS21830409", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33013, "SRR29632275", "SRX25138327", "SRS21830411", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.", null, null, null, "Bmp4 explant 6h", "GSM8366750", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 6h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 \u03bcg/ml gentamycin 100 \u03bcM 2 mercaptoethanol 1\u00d7 antibiotic antimycotic 10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366750", "GSM8366750: Bmp4 explant 6h; Danio rerio; RNA Seq", "GSM8366750 r1", "GSM8366750", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4_6h_S1_L001_R1_001.fastq.gz Bmp4_6h_S1_L001_R2_001.fastq.gz", "fastq fastq", 52586645972.0, 441904588.0, "GSM8366750 r1", "0:28 1:91", "A:14755432217;C:11271293276;G:11858476334;T:14700289448;N:1154697", 28, 91, null, null, 14755432217, 11271293276, 11858476334, 14700289448, 1154697, "SRX25138327", "SRS21830411", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33722, "SRR30640695", "SRX26062515", "SRS22631699", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "WT24hpfcontrol1", null, "breed:natural spawning of AB adults|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:WT24hpfcontrol1 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Wild type zebrafish : 12 embryos in total 2 3mg", "WT24hpfcontrol1 R", "WT24hpfcontrol1 R", "Wild type zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "WT24hpfcontrol1_R1.clean.fq.gz 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developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1MOMutant3", null, "breed:Tg [ef1:Myr Tdtomato]|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1MOMutant3 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of MO morphants zebrafish : 12 embryos in total 2 5mg", "PCM1MOMutant3 R", "PCM1MOMutant3 R", "MO morphants zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1MOMutant3_R1.clean.fq.gz PCM1MOMutant3_R2.clean.fq.gz", "fastq fastq", 6356420208.0, 23407180.0, "PCM1MOMutant3 R1.clean.fq.gz", "0:135.78 1:135.78", "A:1742323782;C:1448163439;G:1451783264;T:1714090084;N:59639", 135, 135, null, null, 1742323782, 1448163439, 1451783264, 1714090084, 59639, "SRX26062514", "SRS22631698", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33724, "SRR30640697", "SRX26062513", "SRS22631697", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1MOMutant2", null, "breed:Tg [ef1:Myr Tdtomato]|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1MOMutant2 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of MO morphants zebrafish : 12 embryos in total 2 4mg", "PCM1MOMutant2 R", "PCM1MOMutant2 R", "MO morphants zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1MOMutant2_R1.clean.fq.gz PCM1MOMutant2_R2.clean.fq.gz", "fastq fastq", 6146772469.0, 22703012.0, "PCM1MOMutant2 R1.clean.fq.gz", "0:135.37 1:135.37", "A:1647298308;C:1435201745;G:1438871965;T:1625343182;N:57269", 135, 135, null, null, 1647298308, 1435201745, 1438871965, 1625343182, 57269, "SRX26062513", "SRS22631697", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33725, "SRR30640698", "SRX26062512", "SRS22631696", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1MOMutant1", null, "breed:Tg [ef1:Myr Tdtomato]|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1MOMutant1 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of MO morphants zebrafish : 12 embryos in total 2 3mg", "PCM1MOMutant1 R", "PCM1MOMutant1 R", "MO morphants zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1MOMutant1_R1.clean.fq.gz PCM1MOMutant1_R2.clean.fq.gz", "fastq fastq", 5701775379.0, 21587297.0, "PCM1MOMutant1 R1.clean.fq.gz", "0:132.06 1:132.06", "A:1578153876;C:1282130829;G:1284978375;T:1556460380;N:51919", 132, 132, null, null, 1578153876, 1282130829, 1284978375, 1556460380, 51919, "SRX26062512", "SRS22631696", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33726, "SRR30640699", "SRX26062511", "SRS22631695", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1KOmutant3", null, "breed:Tg [ef1:Myr Tdtomato]|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1KOmutant3 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of pcm1 KO mutant zebrafish : 12 embryos in total 2 5mg", "PCM1KOmutant3 R", "PCM1KOmutant3 R", "pcm1 KO mutant zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1KOmutant3_R1.clean.fq.gz PCM1KOmutant3_R2.clean.fq.gz", "fastq fastq", 4673179612.0, 17529406.0, "PCM1KOmutant3 R1.clean.fq.gz", "0:133.29 1:133.30", "A:1266929858;C:1078407007;G:1080490713;T:1247307342;N:44692", 133, 133, null, null, 1266929858, 1078407007, 1080490713, 1247307342, 44692, "SRX26062511", "SRS22631695", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33727, "SRR30640700", "SRX26062510", "SRS22631694", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1KOmutant2", null, "breed:Tg [ef1:Myr Tdtomato]|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1KOmutant2 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of pcm1 KO mutant zebrafish : 12 embryos in total 2 4mg", "PCM1KOmutant2 R", "PCM1KOmutant2 R", "pcm1 KO mutant zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1KOmutant2_R1.clean.fq.gz PCM1KOmutant2_R2.clean.fq.gz", "fastq fastq", 6073820902.0, 23767661.0, "PCM1KOmutant2 R1.clean.fq.gz", "0:127.78 1:127.77", "A:1691243395;C:1356197711;G:1357868249;T:1668456939;N:54608", 127, 127, null, null, 1691243395, 1356197711, 1357868249, 1668456939, 54608, "SRX26062510", "SRS22631694", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33728, "SRR30640701", "SRX26062509", "SRS22631693", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1KOmutant1", null, "breed:Tg [ef1:Myr Tdtomato]|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1KOmutant1 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of pcm1 KO mutant zebrafish : 12 embryos in total 2 3mg", "PCM1KOmutant1 R", "PCM1KOmutant1 R", "KO mutant zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1KOmutant1_R1.clean.fq.gz PCM1KOmutant1_R2.clean.fq.gz", "fastq fastq", 6040589500.0, 23826027.0, "PCM1KOmutant1 R1.clean.fq.gz", "0:126.76 1:126.76", "A:1733588631;C:1297359473;G:1301151829;T:1708434373;N:55194", 126, 126, null, null, 1733588631, 1297359473, 1301151829, 1708434373, 55194, "SRX26062509", "SRS22631693", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33729, "SRR30640702", "SRX26062508", "SRS22631692", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1KOcompensate3", null, "breed:Tg [HuC:GFP|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1KOcompensate3 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of pcm1 KO compensate zebrafish : 12 embryos in total 2 5mg", "PCM1KOcompensate3 R", "PCM1KOcompensate3 R", "pcm1 KO compensate zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1KOcompensate3_R1.clean.fq.gz PCM1KOcompensate3_R2.clean.fq.gz", "fastq fastq", 5632945620.0, 21351897.0, "PCM1KOcompensate3 R1.clean.fq.gz", "0:131.92 1:131.90", "A:1561604697;C:1264380828;G:1267746178;T:1539161674;N:52243", 131, 131, null, null, 1561604697, 1264380828, 1267746178, 1539161674, 52243, "SRX26062508", "SRS22631692", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33730, "SRR30640703", "SRX26062507", "SRS22631691", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "WT24hpfcontrol3", null, "breed:natural spawning of AB adults|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:WT24hpfcontrol3 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Wild type zebrafish : 12 embryos in total 2 5mg", "WT24hpfcontrol3 R", "WT24hpfcontrol3 R", "Wild type zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "WT24hpfcontrol3_R1.clean.fq.gz WT24hpfcontrol3_R2.clean.fq.gz", "fastq fastq", 5047867453.0, 19837417.0, "WT24hpfcontrol3 R1.clean.fq.gz", "0:127.23 1:127.23", "A:1412463929;C:1119657233;G:1121642146;T:1394058438;N:45707", 127, 127, null, null, 1412463929, 1119657233, 1121642146, 1394058438, 45707, "SRX26062507", "SRS22631691", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33731, "SRR30640704", "SRX26062506", "SRS22631690", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "WT24hpfcontrol2", null, "breed:natural spawning of AB adults|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:WT24hpfcontrol2 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Wild type zebrafish : 12 embryos in total 2 4mg", "WT24hpfcontrol2 R", "WT24hpfcontrol2 R", "Wild type zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "WT24hpfcontrol2_R1.clean.fq.gz WT24hpfcontrol2_R2.clean.fq.gz", "fastq fastq", 5408273952.0, 21601107.0, "WT24hpfcontrol2 R1.clean.fq.gz", "0:125.19 1:125.18", "A:1510365712;C:1201646307;G:1204419555;T:1491793767;N:48611", 125, 125, null, null, 1510365712, 1201646307, 1204419555, 1491793767, 48611, "SRX26062506", "SRS22631690", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33732, "SRR30640705", "SRX26062505", "SRS22631689", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1KOcompensate2", null, "breed:Tg [HuC:GFP|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1KOcompensate2 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of pcm1 KO compensate zebrafish : 12 embryos in total 2 4mg", "PCM1KOcompensate2 R", "PCM1KOcompensate2 R", "pcm1 KO compensate zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1KOcompensate2_R1.clean.fq.gz PCM1KOcompensate2_R2.clean.fq.gz", "fastq fastq", 5996379188.0, 22765993.0, "PCM1KOcompensate2 R1.clean.fq.gz", "0:131.70 1:131.70", "A:1669800521;C:1339211911;G:1342418096;T:1644890999;N:57661", 131, 131, null, null, 1669800521, 1339211911, 1342418096, 1644890999, 57661, "SRX26062505", "SRS22631689", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [33733, "SRR30640706", "SRX26062504", "SRS22631688", "SRP532179", "PRJNA1159911", "Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate", "PRJNA1159911", "Other", "RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.", null, null, null, null, "PCM1KOcompensate1", null, "breed:Tg [HuC:GFP|age:24hpf|dev stage:adult|collection date:2021 03 19|geo loc name:USA:San Francisco|sex:not determined|tissue:PCM1KOcompensate1 embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of pcm1 KO compensate zebrafish : 12 embryos in total 2 3mg", "PCM1KOcompensate1 R", "PCM1KOcompensate1 R", "pcm1 KO compensate zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 1000", null, "SRP532179", null, null, "PCM1KOcompensate1_R1.clean.fq.gz PCM1KOcompensate1_R2.clean.fq.gz", "fastq fastq", 5594219881.0, 21191291.0, "PCM1KOcompensate1 R1.clean.fq.gz", "0:131.99 1:131.99", "A:1594003450;C:1214578517;G:1215705001;T:1569880851;N:52062", 131, 131, null, null, 1594003450, 1214578517, 1215705001, 1569880851, 52062, "SRX26062504", "SRS22631688", "SRA1970017", "Huazhong Agricultural University, China|Department of Neurosurgery", "Huazhong Agricultural University, China", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-09-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [34688, "SRR32217622", "SRX27557938", "SRS23971739", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish PNP 16hpf 2", "GSM8772774", null, "source name:16 hpf embryos|tissue:16 hpf embryos|genotype:puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish PNP 16hpf 2", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "16 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:16 hpf embryos|genotype:puma / ; noxa / ; p21 / ", "GSM8772774", "GSM8772774: Zebrafish PNP 16hpf 2; Danio rerio; RNA Seq", "GSM8772774 r1", "GSM8772774", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "PNP-16hpf-R2_R1_001.fastq.gz PNP-16hpf-R2_R2_001.fastq.gz", "fastq fastq", 10535154600.0, 35117182.0, "GSM8772774 r1", "0:150 1:150", "A:2785456121;C:2485921943;G:2549544461;T:2712941662;N:1290413", 150, 150, null, null, 2785456121, 2485921943, 2549544461, 2712941662, 1290413, "SRX27557938", "SRS23971739", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34689, "SRR32217623", "SRX27557937", "SRS23971738", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish PNP 16hpf 1", "GSM8772773", null, "source name:16 hpf embryos|tissue:16 hpf embryos|genotype:puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish PNP 16hpf 1", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "16 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:16 hpf embryos|genotype:puma / ; noxa / ; p21 / ", "GSM8772773", "GSM8772773: Zebrafish PNP 16hpf 1; Danio rerio; RNA Seq", "GSM8772773 r1", "GSM8772773", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "PNP-16hpf-R1-LCM9111_L3_R1_001.fastq.gz PNP-16hpf-R1-LCM9111_L3_R2_001.fastq.gz", "fastq fastq", 10601406000.0, 35338020.0, "GSM8772773 r1", "0:150 1:150", "A:2680198721;C:2624253376;G:2633457482;T:2663407541;N:88880", 150, 150, null, null, 2680198721, 2624253376, 2633457482, 2663407541, 88880, "SRX27557937", "SRS23971738", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34690, "SRR32217624", "SRX27557936", "SRS23971737", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish MPNP 16hpf 2", "GSM8772772", null, "source name:16 hpf embryos|tissue:16 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish MPNP 16hpf 2", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "16 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:16 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / ", "GSM8772772", "GSM8772772: Zebrafish MPNP 16hpf 2; Danio rerio; RNA Seq", "GSM8772772 r1", "GSM8772772", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "MPNP-16hpf-R2_R1_001.fastq.gz MPNP-16hpf-R2_R2_001.fastq.gz", "fastq fastq", 14701359300.0, 49004531.0, "GSM8772772 r1", "0:150 1:150", "A:3947459353;C:3409168557;G:3472564779;T:3870403810;N:1762801", 150, 150, null, null, 3947459353, 3409168557, 3472564779, 3870403810, 1762801, "SRX27557936", "SRS23971737", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34691, "SRR32217625", "SRX27557935", "SRS23971736", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish MPNP 16hpf 1", "GSM8772771", null, "source name:16 hpf embryos|tissue:16 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish MPNP 16hpf 1", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "16 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:16 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / ", "GSM8772771", "GSM8772771: Zebrafish MPNP 16hpf 1; Danio rerio; RNA Seq", "GSM8772771 r1", "GSM8772771", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "MPNP-16hpf-R1-LCM9110_L3_R1_001.fastq.gz MPNP-16hpf-R1-LCM9110_L3_R2_001.fastq.gz", "fastq fastq", 10235183700.0, 34117279.0, "GSM8772771 r1", "0:150 1:150", "A:2570056156;C:2549706468;G:2564252810;T:2551084265;N:84001", 150, 150, null, null, 2570056156, 2549706468, 2564252810, 2551084265, 84001, "SRX27557935", "SRS23971736", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34692, "SRR32217629", "SRX27557934", "SRS23971735", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish PNP 14hpf 2", "GSM8772770", null, "source name:14 hpf embryos|tissue:14 hpf embryos|genotype:puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish PNP 14hpf 2", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "14 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:14 hpf embryos|genotype:puma / ; noxa / ; p21 / ", "GSM8772770", "GSM8772770: Zebrafish PNP 14hpf 2; Danio rerio; RNA Seq", "GSM8772770 r1", "GSM8772770", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "PNP-14hpf-R2_R1_001.fastq.gz PNP-14hpf-R2_R2_001.fastq.gz", "fastq fastq", 5414434800.0, 18048116.0, "GSM8772770 r1", "0:150 1:150", "A:1444381230;C:1263354350;G:1292187383;T:1413874437;N:637400", 150, 150, null, null, 1444381230, 1263354350, 1292187383, 1413874437, 637400, "SRX27557934", "SRS23971735", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34693, "SRR32217626", "SRX27557933", "SRS23971734", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish PNP 14hpf 1", "GSM8772769", null, "source name:14 hpf embryos|tissue:14 hpf embryos|genotype:puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish PNP 14hpf 1", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "14 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:14 hpf embryos|genotype:puma / ; noxa / ; p21 / ", "GSM8772769", "GSM8772769: Zebrafish PNP 14hpf 1; Danio rerio; RNA Seq", "GSM8772769 r1", "GSM8772769", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "PNP-14hpf-R1-LCM9109_L3_R1_001.fastq.gz PNP-14hpf-R1-LCM9109_L3_R2_001.fastq.gz", "fastq fastq", 9851333400.0, 32837778.0, "GSM8772769 r1", "0:150 1:150", "A:2483678308;C:2443272708;G:2457808801;T:2466491868;N:81715", 150, 150, null, null, 2483678308, 2443272708, 2457808801, 2466491868, 81715, "SRX27557933", "SRS23971734", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34694, "SRR32217627", "SRX27557932", "SRS23971733", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish MPNP 14hpf 2", "GSM8772768", null, "source name:14 hpf embryos|tissue:14 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish MPNP 14hpf 2", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "14 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:14 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / ", "GSM8772768", "GSM8772768: Zebrafish MPNP 14hpf 2; Danio rerio; RNA Seq", "GSM8772768 r1", "GSM8772768", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "MPNP-14hpf-R2_R1_001.fastq.gz MPNP-14hpf-R2_R2_001.fastq.gz", "fastq fastq", 5953892700.0, 19846309.0, "GSM8772768 r1", "0:150 1:150", "A:1597853468;C:1382446019;G:1420097871;T:1552767183;N:728159", 150, 150, null, null, 1597853468, 1382446019, 1420097871, 1552767183, 728159, "SRX27557932", "SRS23971733", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34695, "SRR32217628", "SRX27557931", "SRS23971732", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish MPNP 14hpf 1", "GSM8772767", null, "source name:14 hpf embryos|tissue:14 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish MPNP 14hpf 1", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "14 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:14 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / ", "GSM8772767", "GSM8772767: Zebrafish MPNP 14hpf 1; Danio rerio; RNA Seq", "GSM8772767 r1", "GSM8772767", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "MPNP-14hpf-R1-LCM9108_L3_R1_001.fastq.gz MPNP-14hpf-R1-LCM9108_L3_R2_001.fastq.gz", "fastq fastq", 11636365200.0, 38787884.0, "GSM8772767 r1", "0:150 1:150", "A:2939300419;C:2879587889;G:2900004636;T:2917376468;N:95788", 150, 150, null, null, 2939300419, 2879587889, 2900004636, 2917376468, 95788, "SRX27557931", "SRS23971732", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34696, "SRR32217630", "SRX27557930", "SRS23971731", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish PNP 12hpf 2", "GSM8772766", null, "source name:12 hpf embryos|tissue:12 hpf embryos|genotype:puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish PNP 12hpf 2", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "12 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:12 hpf embryos|genotype:puma / ; noxa / ; p21 / ", "GSM8772766", "GSM8772766: Zebrafish PNP 12hpf 2; Danio rerio; RNA Seq", "GSM8772766 r1", "GSM8772766", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "PNP-12hpf-R2_R1_001.fastq.gz PNP-12hpf-R2_R2_001.fastq.gz", "fastq fastq", 11432631000.0, 38108770.0, "GSM8772766 r1", "0:150 1:150", "A:3080886583;C:2644530522;G:2728628121;T:2977190031;N:1395743", 150, 150, null, null, 3080886583, 2644530522, 2728628121, 2977190031, 1395743, "SRX27557930", "SRS23971731", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34697, "SRR32217631", "SRX27557929", "SRS23971730", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish PNP 12hpf 1", "GSM8772765", null, "source name:12 hpf embryos|tissue:12 hpf embryos|genotype:puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish PNP 12hpf 1", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "12 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:12 hpf embryos|genotype:puma / ; noxa / ; p21 / ", "GSM8772765", "GSM8772765: Zebrafish PNP 12hpf 1; Danio rerio; RNA Seq", "GSM8772765 r1", "GSM8772765", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "PNP-12hpf-R1-LCM9107_L3_R1_001.fastq.gz PNP-12hpf-R1-LCM9107_L3_R2_001.fastq.gz", "fastq fastq", 10479699900.0, 34932333.0, "GSM8772765 r1", "0:150 1:150", "A:2633044362;C:2608423365;G:2628903024;T:2609268781;N:60368", 150, 150, null, null, 2633044362, 2608423365, 2628903024, 2609268781, 60368, "SRX27557929", "SRS23971730", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34698, "SRR32217632", "SRX27557928", "SRS23971729", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish MPNP 12hpf 2", "GSM8772764", null, "source name:12 hpf embryos|tissue:12 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish MPNP 12hpf 2", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "12 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:12 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / ", "GSM8772764", "GSM8772764: Zebrafish MPNP 12hpf 2; Danio rerio; RNA Seq", "GSM8772764 r1", "GSM8772764", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "MPNP-12hpf-R2_R1_001.fastq.gz MPNP-12hpf-R2_R2_001.fastq.gz", "fastq fastq", 13955378700.0, 46517929.0, "GSM8772764 r1", "0:150 1:150", "A:3763427959;C:3222562735;G:3362175176;T:3605511213;N:1701617", 150, 150, null, null, 3763427959, 3222562735, 3362175176, 3605511213, 1701617, "SRX27557928", "SRS23971729", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34699, "SRR32217633", "SRX27557927", "SRS23971728", "SRP561364", "PRJNA1218816", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]", "GSE288666", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately \u00bc of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.", null, "pubmed:40487439", null, "Zebrafish MPNP 12hpf 1", "GSM8772763", null, "source name:12 hpf embryos|tissue:12 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish MPNP 12hpf 1", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "12 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:12 hpf embryos|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / ", "GSM8772763", "GSM8772763: Zebrafish MPNP 12hpf 1; Danio rerio; RNA Seq", "GSM8772763 r1", "GSM8772763", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561364", null, null, "MPNP-12hpf-R1-LCM9106_L3_R1_001.fastq.gz MPNP-12hpf-R1-LCM9106_L3_R2_001.fastq.gz", "fastq fastq", 10563368700.0, 35211229.0, "GSM8772763 r1", "0:150 1:150", "A:2677547502;C:2602743506;G:2625615434;T:2657374696;N:87562", 150, 150, null, null, 2677547502, 2602743506, 2625615434, 2657374696, 87562, "SRX27557927", "SRS23971728", "SRA2069214", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34708, "SRR32217642", "SRX27557942", "SRS23971743", "SRP561365", "PRJNA1218818", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf]", "GSE288667", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison.", null, "pubmed:40487439", null, "Zebrafish Normal PNP 18hpf 2", "GSM8772778", null, "source name:30 hpf embryos|tissue:30 hpf embryos|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish Normal PNP 18hpf 2", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "30 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:30 hpf embryos|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 / ", "GSM8772778", "GSM8772778: Zebrafish Normal PNP 18hpf 2; Danio rerio; RNA Seq", "GSM8772778 r1", "GSM8772778", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561365", null, null, "PNP-18hpf-R2-LCM9117_L3_R1_001 PNP-18hpf-R2-LCM9117_L3_R2_001", "fastq fastq", 11448228300.0, 38160761.0, "GSM8772778 r1", "0:150 1:150", "A:2869273191;C:2853873509;G:2871650417;T:2853336221;N:94962", 150, 150, null, null, 2869273191, 2853873509, 2871650417, 2853336221, 94962, "SRX27557942", "SRS23971743", "SRA2069215", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34709, "SRR32217643", "SRX27557941", "SRS23971742", "SRP561365", "PRJNA1218818", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf]", "GSE288667", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison.", null, "pubmed:40487439", null, "Zebrafish Normal PNP 18hpf 1", "GSM8772777", null, "source name:30 hpf embryos|tissue:30 hpf embryos|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish Normal PNP 18hpf 1", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "30 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:30 hpf embryos|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 / ", "GSM8772777", "GSM8772777: Zebrafish Normal PNP 18hpf 1; Danio rerio; RNA Seq", "GSM8772777 r1", "GSM8772777", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561365", null, null, "PNP-18hpf-R1-LCM9116_L3_R1_001 PNP-18hpf-R1-LCM9116_L3_R2_001", "fastq fastq", 10028796900.0, 33429323.0, "GSM8772777 r1", "0:150 1:150", "A:2522600143;C:2493920962;G:2504259374;T:2507933554;N:82867", 150, 150, null, null, 2522600143, 2493920962, 2504259374, 2507933554, 82867, "SRX27557941", "SRS23971742", "SRA2069215", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34710, "SRR32217644", "SRX27557940", "SRS23971741", "SRP561365", "PRJNA1218818", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf]", "GSE288667", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison.", null, "pubmed:40487439", null, "Zebrafish Abnormal MPNP 18hpf 2", "GSM8772776", null, "source name:30 hpf embryos|tissue:30 hpf embryos|genotype:mdm2 / ; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish Abnormal MPNP 18hpf 2", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "30 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:30 hpf embryos|genotype:mdm2 / ; puma / ; noxa / ; p21 / ", "GSM8772776", "GSM8772776: Zebrafish Abnormal MPNP 18hpf 2; Danio rerio; RNA Seq", "GSM8772776 r1", "GSM8772776", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561365", null, null, "MPNP-Abnor-18hpf-R2-LCM9115_L3_R1_001 MPNP-Abnor-18hpf-R2-LCM9115_L3_R2_001", "fastq fastq", 9458944500.0, 31529815.0, "GSM8772776 r1", "0:150 1:150", "A:2402362356;C:2327441574;G:2341949851;T:2387110941;N:79778", 150, 150, null, null, 2402362356, 2327441574, 2341949851, 2387110941, 79778, "SRX27557940", "SRS23971741", "SRA2069215", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34711, "SRR32217645", "SRX27557939", "SRS23971740", "SRP561365", "PRJNA1218818", "p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf]", "GSE288667", "Transcriptome Analysis", "p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 \u201ccrispant\u201d screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison.", null, "pubmed:40487439", null, "Zebrafish Abnormal MPNP 18hpf 1", "GSM8772775", null, "source name:30 hpf embryos|tissue:30 hpf embryos|genotype:mdm2 / ; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing", "Zebrafish Abnormal MPNP 18hpf 1", "Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples", "30 hpf embryos", null, "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer\u2019s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", "The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.", "tissue:30 hpf embryos|genotype:mdm2 / ; puma / ; noxa / ; p21 / ", "GSM8772775", "GSM8772775: Zebrafish Abnormal MPNP 18hpf 1; Danio rerio; RNA Seq", "GSM8772775 r1", "GSM8772775", "1", "Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP561365", null, null, "MPNP-Abnor-18hpf-R1-LCM9114_L3_R1_001 MPNP-Abnor-18hpf-R1-LCM9114_L3_R2_001", "fastq fastq", 10085728800.0, 33619096.0, "GSM8772775 r1", "0:150 1:150", "A:2514952200;C:2527390008;G:2540349801;T:2502952120;N:84671", 150, 150, null, null, 2514952200, 2527390008, 2540349801, 2502952120, 84671, "SRX27557939", "SRS23971740", "SRA2069215", "University of Alabama at Birmingham", "University of Alabama at Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-02-03", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35389, "SRR32737834", "SRX28024098", "SRS24385653", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851836", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851836", "GSM8851836: replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851836 r1", "GSM8851836", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R7OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R7OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 18969663600.0, 63232212.0, "GSM8851836 r1", "0:150 1:150", "A:5368170604;C:4078596357;G:4113230716;T:5408149968;N:1515955", 150, 150, null, null, 5368170604, 4078596357, 4113230716, 5408149968, 1515955, "SRX28024098", "SRS24385653", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35390, "SRR32737835", "SRX28024097", "SRS24385650", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851835", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851835", "GSM8851835: replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851835 r1", "GSM8851835", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R5OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R5OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 19589608200.0, 65298694.0, "GSM8851835 r1", "0:150 1:150", "A:5414548081;C:4374558112;G:4362382403;T:5436601325;N:1518279", 150, 150, null, null, 5414548081, 4374558112, 4362382403, 5436601325, 1518279, "SRX28024097", "SRS24385650", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35391, "SRR32737836", "SRX28024096", "SRS24385649", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851834", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851834", "GSM8851834: replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851834 r1", "GSM8851834", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 19946087100.0, 66486957.0, "GSM8851834 r1", "0:150 1:150", "A:5380413495;C:4584083127;G:4577230707;T:5402765142;N:1594629", 150, 150, null, null, 5380413495, 4584083127, 4577230707, 5402765142, 1594629, "SRX28024096", "SRS24385649", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35392, "SRR32737837", "SRX28024095", "SRS24385647", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851833", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851833", "GSM8851833: replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851833 r1", "GSM8851833", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 12448266300.0, 41494221.0, "GSM8851833 r1", "0:150 1:150", "A:3395623757;C:2824144586;G:2822937408;T:3404571425;N:989124", 150, 150, null, null, 3395623757, 2824144586, 2822937408, 3404571425, 989124, "SRX28024095", "SRS24385647", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35393, "SRR32737838", "SRX28024094", "SRS24385648", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851832", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851832", "GSM8851832: replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851832 r1", "GSM8851832", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R1OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 19798955700.0, 65996519.0, "GSM8851832 r1", "0:150 1:150", "A:5229008693;C:4668558136;G:4674407786;T:5225398568;N:1582517", 150, 150, null, null, 5229008693, 4668558136, 4674407786, 5225398568, 1582517, "SRX28024094", "SRS24385648", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35394, "SRR32737842", "SRX28024093", "SRS24385646", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851831", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851831", "GSM8851831: replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851831 r1", "GSM8851831", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R6OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R6OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 18130666800.0, 60435556.0, "GSM8851831 r1", "0:150 1:150", "A:4966144411;C:4092769735;G:4085294185;T:4985017148;N:1441321", 150, 150, null, null, 4966144411, 4092769735, 4085294185, 4985017148, 1441321, "SRX28024093", "SRS24385646", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35395, "SRR32737839", "SRX28024092", "SRS24385645", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851830", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851830", "GSM8851830: replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851830 r1", "GSM8851830", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 19991640600.0, 66638802.0, "GSM8851830 r1", "0:150 1:150", "A:5447335535;C:4526376231;G:4535727704;T:5480632098;N:1569032", 150, 150, null, null, 5447335535, 4526376231, 4535727704, 5480632098, 1569032, "SRX28024092", "SRS24385645", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35396, "SRR32737840", "SRX28024091", "SRS24385644", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851829", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851829", "GSM8851829: replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851829 r1", "GSM8851829", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R3OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R3OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 22065261900.0, 73550873.0, "GSM8851829 r1", "0:150 1:150", "A:5991325177;C:5034454094;G:5016024645;T:6021738394;N:1719590", 150, 150, null, null, 5991325177, 5034454094, 5016024645, 6021738394, 1719590, "SRX28024091", "SRS24385644", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35397, "SRR32737841", "SRX28024090", "SRS24385643", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851828", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851828", "GSM8851828: replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851828 r1", "GSM8851828", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 14038941600.0, 46796472.0, "GSM8851828 r1", "0:150 1:150", "A:3916268130;C:3079070561;G:3101493441;T:3941005195;N:1104273", 150, 150, null, null, 3916268130, 3079070561, 3101493441, 3941005195, 1104273, "SRX28024090", "SRS24385643", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35398, "SRR32737843", "SRX28024089", "SRS24385641", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851827", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851827", "GSM8851827: replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851827 r1", "GSM8851827", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R1OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 13386761100.0, 44622537.0, "GSM8851827 r1", "0:150 1:150", "A:3794190335;C:2871376272;G:2905470401;T:3814688762;N:1035330", 150, 150, null, null, 3794190335, 2871376272, 2905470401, 3814688762, 1035330, "SRX28024089", "SRS24385641", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35399, "SRR32737844", "SRX28024088", "SRS24385642", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851826", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851826", "GSM8851826: replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851826 r1", "GSM8851826", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R6FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R6FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 21105961200.0, 70353204.0, "GSM8851826 r1", "0:150 1:150", "A:5809999918;C:4738287088;G:4727306148;T:5828688062;N:1679984", 150, 150, null, null, 5809999918, 4738287088, 4727306148, 5828688062, 1679984, "SRX28024088", "SRS24385642", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35400, "SRR32737845", "SRX28024087", "SRS24385640", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851825", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851825", "GSM8851825: replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851825 r1", "GSM8851825", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R5FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R5FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 23123472900.0, 77078243.0, "GSM8851825 r1", "0:150 1:150", "A:6076414910;C:5484056288;G:5478904909;T:6082279094;N:1817699", 150, 150, null, null, 6076414910, 5484056288, 5478904909, 6082279094, 1817699, "SRX28024087", "SRS24385640", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35401, "SRR32737846", "SRX28024086", "SRS24385638", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851824", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851824", "GSM8851824: replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851824 r1", "GSM8851824", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 21177911700.0, 70593039.0, "GSM8851824 r1", "0:150 1:150", "A:5565860585;C:5018913046;G:5013238014;T:5578213850;N:1686205", 150, 150, null, null, 5565860585, 5018913046, 5013238014, 5578213850, 1686205, "SRX28024086", "SRS24385638", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35402, "SRR32737850", "SRX28024085", "SRS24385639", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851823", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851823", "GSM8851823: replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851823 r1", "GSM8851823", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 23561164500.0, 78537215.0, "GSM8851823 r1", "0:150 1:150", "A:7284568054;C:4438434312;G:4560720005;T:7275566382;N:1875747", 150, 150, null, null, 7284568054, 4438434312, 4560720005, 7275566382, 1875747, "SRX28024085", "SRS24385639", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35403, "SRR32737847", "SRX28024084", "SRS24385637", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851822", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851822", "GSM8851822: replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851822 r1", "GSM8851822", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R1FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 11262181200.0, 37540604.0, "GSM8851822 r1", "0:150 1:150", "A:3084661516;C:2546033080;G:2544910194;T:3085685271;N:891139", 150, 150, null, null, 3084661516, 2546033080, 2544910194, 3085685271, 891139, "SRX28024084", "SRS24385637", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35404, "SRR32737848", "SRX28024083", "SRS24385636", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq.", null, "pubmed:40429979", null, "replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851821", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024", "GSM8851821", "GSM8851821: replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851821 r1", "GSM8851821", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R7FE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R7FE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 15368398200.0, 51227994.0, "GSM8851821 r1", "0:150 1:150", "A:4439560630;C:3205670434;G:3245419161;T:4476535407;N:1212568", 150, 150, null, null, 4439560630, 3205670434, 3245419161, 4476535407, 1212568, "SRX28024083", "SRS24385636", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 1838, "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", 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