rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
9898,ERR4194114,ERX4155254,ERS4601292,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA8h_1_S2_L001.bam,bam,10087287534.0,99874134.0,E MTAB 9193:cDNA8h 1 S2 L001,0:101,A:2892833391;C:2022466595;G:2198646699;T:2962268446;N:11072403,101,,,,2892833391,2022466595,2198646699,2962268446,11072403,ERX4155254,ERS4601292,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93609,,0.12902,,0.82158,,0.5062,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9899,ERR4194115,ERX4155254,ERS4601292,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.13038,,0.824,,0.49774,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.12156,,0.8117,,0.51457,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.12127,,0.81162,,0.51457,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.07571,,0.92951,,0.5272,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.08054,,0.91583,,0.52661,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.13033,,0.89132,,0.47076,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.13128,,0.89923,,0.46879,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.12965,,0.91265,,0.47375,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.1266,,0.87714,,0.46957,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.10744,,0.81984,,0.501,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.10818,,0.82211,,0.50079,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.10645,,0.82329,,0.50057,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.10842,,0.82031,,0.49241,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.10719,,0.8238,,0.50406,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.10675,,0.82079,,0.49284,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.10749,,0.82266,,0.49382,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.10755,,0.82158,,0.49895,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.08039,,0.93026,,0.50796,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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 μl 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 μm 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,,,,,,,,,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 μl 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 μm 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,,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,,,,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,,0.08597,,0.91804,,0.51772,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
10186,ERR6212423,ERX5847531,ERS7094943,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Naive,SAMEA9361876,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Naive p,Naive p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz,fastq fastq fastq,60168324125.0,481346593.0,E MTAB 10379 3:Naive,0:8 1:27 2:90,A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241,8,27,90,,12424400694,9366563781,10029312355,11497237299,3679241,ERX5847531,ERS7094943,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.94834,,0.09482,,0.802,,0.5277,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
10187,ERR6212422,ERX5847530,ERS7094942,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Lesi1d,SAMEA9361875,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Lesioned p,Lesioned p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:spinal cord lesion,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz,fastq fastq fastq,61701873000.0,493614984.0,E MTAB 10379 3:Lesioned,0:8 1:27 2:90,A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277,8,27,90,,12952533019,9222397450,9920185920,12326470894,3761277,ERX5847530,ERS7094942,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.93082,,0.10862,,0.80302,,0.54924,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
11017,ERR9750937,ERX9298876,ERS12023662,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 Uninjured,SAMEA14418104,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418104|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 2 Uninjured|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 Uninjured p,Expt 2 Uninjured p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:n1|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_Uninjured_S2_L002_I1_001.fastq.gz E2_Uninjured_S2_L002_I2_001.fastq.gz E2_Uninjured_S2_L002_R1_001.fastq.gz E2_Uninjured_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9325673775.0,69079065.0,E MTAB 10643:Expt 2 Uninjured,0:10 1:10 2:28 3:87,A:1619571910;C:1420805235;G:1471531128;T:1496998088;N:972294,10,10,28,87,1619571910,1420805235,1471531128,1496998088,972294,ERX9298876,ERS12023662,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.93798,,0.11364,,0.84843,,0.53531,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11018,ERR9750936,ERX9298875,ERS12023661,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 Sham,SAMEA14418103,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418103|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Sham|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:sham surgery|organism part:heart|sample name:E MTAB 10643:Expt 2 Sham|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 Sham p,Expt 2 Sham p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:sham surgery|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_Sham_S1_L002_I1_001.fastq.gz E2_Sham_S1_L002_I2_001.fastq.gz E2_Sham_S1_L002_R1_001.fastq.gz E2_Sham_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11328674040.0,83916104.0,E MTAB 10643:Expt 2 Sham,0:10 1:10 2:28 3:87,A:1955327720;C:1746332187;G:1777122701;T:1820705338;N:1213102,10,10,28,87,1955327720,1746332187,1777122701,1820705338,1213102,ERX9298875,ERS12023661,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.92847,,0.09981,,0.85707,,0.46947,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11019,ERR9750935,ERX9298874,ERS12023660,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 3d post amputation,SAMEA14418102,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418102|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 2 3d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 3d post amputation p,Expt 2 3d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_3dpa_S3_L002_I1_001.fastq.gz E2_3dpa_S3_L002_I2_001.fastq.gz E2_3dpa_S3_L002_R1_001.fastq.gz E2_3dpa_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,16111486440.0,119344344.0,E MTAB 10643:Expt 2 3d post amputation,0:10 1:10 2:28 3:87,A:2610144058;C:2617445332;G:2496763759;T:2656876552;N:1728227,10,10,28,87,2610144058,2617445332,2496763759,2656876552,1728227,ERX9298874,ERS12023660,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.94868,,0.07071,,0.89221,,0.54333,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11020,ERR9750934,ERX9298873,ERS12023659,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 3 3d post amputation + MMP inhibitor,SAMEA14418101,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418101|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|sex:male|strain:AB|treatment:matrix metalloproteinase inhibitor,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor p,Expt 3 3d post amputation + MMP inhibitor p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:matrix metalloproteinase inhibitor,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_3dpa_inhibitor_S4_L002_I1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_I2_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8621019270.0,63859402.0,E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor,0:10 1:10 2:28 3:87,A:1438763050;C:1365497247;G:1350808021;T:1399773154;N:926502,10,10,28,87,1438763050,1365497247,1350808021,1399773154,926502,ERX9298873,ERS12023659,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.92796,,0.08671,,0.87176,,0.55088,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11021,ERR9750933,ERX9298872,ERS12023658,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 Uninjured,SAMEA14418100,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418100|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 1 Uninjured|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 Uninjured p,Expt 1 Uninjured p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:n1|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_Uninjured_S1_L002_I1_001.fastq.gz E1_Uninjured_S1_L002_R1_001.fastq.gz E1_Uninjured_S1_L002_R2_001.fastq.gz,fastq fastq fastq,8575585211.0,67524293.0,E MTAB 10643:Expt 1 Uninjured,0:8 1:28 2:91,A:1801503847;C:1312196506;G:1367890726;T:1663053783;N:65801,8,28,91,,1801503847,1312196506,1367890726,1663053783,65801,ERX9298872,ERS12023658,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.9169,,0.11202,,0.81576,,0.54253,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11022,ERR9750932,ERX9298871,ERS12023657,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 7d post amputation,SAMEA14418099,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418099|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 7d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 7d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 7d post amputation p,Expt 1 7d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:7|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_7d_S3_L002_I1_001.fastq.gz E1_7d_S3_L002_R1_001.fastq.gz E1_7d_S3_L002_R2_001.fastq.gz,fastq fastq fastq,17341796660.0,136549580.0,E MTAB 10643:Expt 1 7d post amputation,0:8 1:28 2:91,A:3506600812;C:2774617588;G:2814960106;T:3329701112;N:132162,8,28,91,,3506600812,2774617588,2814960106,3329701112,132162,ERX9298871,ERS12023657,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.90616,,0.09608,,0.82446,,0.46632,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11023,ERR9750931,ERX9298870,ERS12023656,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 3d post amputation,SAMEA14418098,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418098|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 3d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 3d post amputation p,Expt 1 3d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_3d_S2_L002_I1_001.fastq.gz E1_3d_S2_L002_R1_001.fastq.gz E1_3d_S2_L002_R2_001.fastq.gz,fastq fastq fastq,8183008018.0,64433134.0,E MTAB 10643:Expt 1 3d post amputation,0:8 1:28 2:91,A:1630460899;C:1330248096;G:1326144211;T:1576499358;N:62630,8,28,91,,1630460899,1330248096,1326144211,1576499358,62630,ERX9298870,ERS12023656,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.88759,,0.08679,,0.82948,,0.47863,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11024,ERR9750930,ERX9298869,ERS12023655,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 14d post amputation,SAMEA14418097,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418097|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 14d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 14d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 14d post amputation p,Expt 1 14d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:14|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_14d_S4_L002_I1_001.fastq.gz E1_14d_S4_L002_R1_001.fastq.gz E1_14d_S4_L002_R2_001.fastq.gz,fastq fastq fastq,12911908390.0,101668570.0,E MTAB 10643:Expt 1 14d post amputation,0:8 1:28 2:91,A:2700371496;C:1971281481;G:2062280628;T:2517806408;N:99857,8,28,91,,2700371496,1971281481,2062280628,2517806408,99857,ERX9298869,ERS12023655,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.90771,,0.11048,,0.81523,,0.53024,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
25107,SRR25605432,SRX21332628,SRS18578260,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep3,GSM7702835,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702835,GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq,GSM7702835 r1,GSM7702835,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_GFP_pos_S4_L001_R2_001.fastq.gz 2707_GFP_pos_S4_L001_R1_001.fastq.gz 2707_GFP_pos_S4_L001_I2_001.fastq.gz 2707_GFP_pos_S4_L001_I1_001.fastq.gz,fastq fastq fastq fastq,21603309774.0,156545723.0,GSM7702835 r1,0:10 1:10 2:28 3:90,A:3960451458;C:3105338977;G:3480072824;T:3541218595;N:2033216,10,10,28,90,3960451458,3105338977,3480072824,3541218595,2033216,SRX21332628,SRS18578260,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94286,,0.14175,,0.78395,,0.51541,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25108,SRR25605433,SRX21332628,SRS18578260,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep3,GSM7702835,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702835,GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq,GSM7702835 r1,GSM7702835,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_GFP_pos_S4_L002_I1_001.fastq.gz 2707_GFP_pos_S4_L002_I2_001.fastq.gz 2707_GFP_pos_S4_L002_R1_001.fastq.gz 2707_GFP_pos_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,22413465270.0,162416415.0,GSM7702835 r2,0:10 1:10 2:28 3:90,A:4104405257;C:3220235633;G:3625448968;T:3667329471;N:58021,10,10,28,90,4104405257,3220235633,3625448968,3667329471,58021,SRX21332628,SRS18578260,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94239,,0.14234,,0.78338,,0.50616,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25109,SRR25822232,SRX21332628,SRS18578260,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep3,GSM7702835,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702835,GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq,GSM7702835 r1,GSM7702835,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_GFP_pos_S4_L001_R2_002.fastq.gz 2707_GFP_pos_S4_L001_R1_002.fastq.gz 2707_GFP_pos_S4_L001_I2_002.fastq.gz 2707_GFP_pos_S4_L001_I1_002.fastq.gz,fastq fastq fastq fastq,21424338264.0,155248828.0,GSM7702835 r3,0:10 1:10 2:28 3:90,A:3928077020;C:3077672525;G:3451667186;T:3513734857;N:1242932,10,10,28,90,3928077020,3077672525,3451667186,3513734857,1242932,SRX21332628,SRS18578260,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.9433,,0.14242,,0.78328,,0.52384,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25110,SRR25822233,SRX21332628,SRS18578260,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep3,GSM7702835,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702835,GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq,GSM7702835 r1,GSM7702835,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_GFP_pos_S4_L002_I1_002.fastq.gz 2707_GFP_pos_S4_L002_I2_002.fastq.gz 2707_GFP_pos_S4_L002_R1_002.fastq.gz 2707_GFP_pos_S4_L002_R2_002.fastq.gz,fastq fastq fastq fastq,22542479952.0,163351304.0,GSM7702835 r4,0:10 1:10 2:28 3:90,A:4130174287;C:3235362228;G:3643457599;T:3691295761;N:1327485,10,10,28,90,4130174287,3235362228,3643457599,3691295761,1327485,SRX21332628,SRS18578260,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94183,,0.14124,,0.78301,,0.50517,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25111,SRR25605434,SRX21332627,SRS18578259,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep3,GSM7702834,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702834,GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq,GSM7702834 r1,GSM7702834,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_pos_Mcherry_S3_L001_R2_001.fastq.gz 2707_pos_Mcherry_S3_L001_R1_001.fastq.gz 2707_pos_Mcherry_S3_L001_I2_001.fastq.gz 2707_pos_Mcherry_S3_L001_I1_001.fastq.gz,fastq fastq fastq fastq,20161522758.0,146097991.0,GSM7702834 r1,0:10 1:10 2:28 3:90,A:3649819934;C:2958286158;G:3267504300;T:3271384686;N:1824112,10,10,28,90,3649819934,2958286158,3267504300,3271384686,1824112,SRX21332627,SRS18578259,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94851,,0.1483,,0.80012,,0.52549,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25112,SRR25605435,SRX21332627,SRS18578259,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep3,GSM7702834,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702834,GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq,GSM7702834 r1,GSM7702834,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_pos_Mcherry_S3_L002_I1_001.fastq.gz 2707_pos_Mcherry_S3_L002_I2_001.fastq.gz 2707_pos_Mcherry_S3_L002_R1_001.fastq.gz 2707_pos_Mcherry_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,20708273928.0,150059956.0,GSM7702834 r2,0:10 1:10 2:28 3:90,A:3746088654;C:3037032642;G:3368938151;T:3353289242;N:47351,10,10,28,90,3746088654,3037032642,3368938151,3353289242,47351,SRX21332627,SRS18578259,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94778,,0.14581,,0.80028,,0.52885,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25113,SRR25822230,SRX21332627,SRS18578259,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep3,GSM7702834,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702834,GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq,GSM7702834 r1,GSM7702834,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_pos_Mcherry_S3_L001_I1_002.fastq.gz 2707_pos_Mcherry_S3_L001_I2_002.fastq.gz 2707_pos_Mcherry_S3_L001_R1_002.fastq.gz 2707_pos_Mcherry_S3_L001_R2_002.fastq.gz,fastq fastq fastq fastq,20078121078.0,145493631.0,GSM7702834 r3,0:10 1:10 2:28 3:90,A:3634984131;C:2943891505;G:3255149272;T:3259243920;N:1157962,10,10,28,90,3634984131,2943891505,3255149272,3259243920,1157962,SRX21332627,SRS18578259,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94884,,0.14622,,0.80099,,0.52572,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25114,SRR25822231,SRX21332627,SRS18578259,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep3,GSM7702834,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702834,GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq,GSM7702834 r1,GSM7702834,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_pos_Mcherry_S3_L002_I1_002.fastq.gz 2707_pos_Mcherry_S3_L002_I2_002.fastq.gz 2707_pos_Mcherry_S3_L002_R1_002.fastq.gz 2707_pos_Mcherry_S3_L002_R2_002.fastq.gz,fastq fastq fastq fastq,20884392978.0,151336181.0,GSM7702834 r4,0:10 1:10 2:28 3:90,A:3779370721;C:3059502508;G:3396295214;T:3383865877;N:1221970,10,10,28,90,3779370721,3059502508,3396295214,3383865877,1221970,SRX21332627,SRS18578259,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94896,,0.14559,,0.8002,,0.51418,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25115,SRR25605436,SRX21332626,SRS18578258,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep2,GSM7702833,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702833,GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq,GSM7702833 r1,GSM7702833,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py|options:  allowEarlyFileEnd,1907_GFP_pos_S2_L001_I1_001.fastq.gz 1907_GFP_pos_S2_L001_I2_001.fastq.gz 1907_GFP_pos_S2_L001_R1_001.fastq.gz 1907_GFP_pos_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,22174775364.0,160686778.0,GSM7702833 r1,0:10 1:10 2:28 3:90,A:4207510387;C:3050740898;G:3362227609;T:3839333241;N:1997885,10,10,28,90,4207510387,3050740898,3362227609,3839333241,1997885,SRX21332626,SRS18578258,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.93287,,0.11844,,0.81087,,0.55264,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25116,SRR25605437,SRX21332626,SRS18578258,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep2,GSM7702833,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702833,GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq,GSM7702833 r1,GSM7702833,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py|options:  allowEarlyFileEnd,1907_GFP_pos_S2_L002_I1_001.fastq.gz 1907_GFP_pos_S2_L002_I2_001.fastq.gz 1907_GFP_pos_S2_L002_R1_001.fastq.gz 1907_GFP_pos_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,22047847518.0,159767011.0,GSM7702833 r2,0:10 1:10 2:28 3:90,A:4174013532;C:3033959926;G:3357962867;T:3813042664;N:52001,10,10,28,90,4174013532,3033959926,3357962867,3813042664,52001,SRX21332626,SRS18578258,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.93359,,0.11585,,0.81087,,0.55705,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25117,SRR25822228,SRX21332626,SRS18578258,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep2,GSM7702833,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702833,GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq,GSM7702833 r1,GSM7702833,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_GFP_pos_S2_L001_I1_002.fastq.gz 1907_GFP_pos_S2_L001_I2_002.fastq.gz 1907_GFP_pos_S2_L001_R1_002.fastq.gz 1907_GFP_pos_S2_L001_R2_002.fastq.gz,fastq fastq fastq fastq,22010894568.0,159499236.0,GSM7702833 r3,0:10 1:10 2:28 3:90,A:4176090595;C:3026940106;G:3336506731;T:3814128890;N:1264918,10,10,28,90,4176090595,3026940106,3336506731,3814128890,1264918,SRX21332626,SRS18578258,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.93457,,0.11733,,0.81032,,0.55203,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25118,SRR25822229,SRX21332626,SRS18578258,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep2,GSM7702833,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702833,GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq,GSM7702833 r1,GSM7702833,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_GFP_pos_S2_L002_I1_002.fastq.gz 1907_GFP_pos_S2_L002_I2_002.fastq.gz 1907_GFP_pos_S2_L002_R1_002.fastq.gz 1907_GFP_pos_S2_L002_R2_002.fastq.gz,fastq fastq fastq fastq,22227220746.0,161066817.0,GSM7702833 r4,0:10 1:10 2:28 3:90,A:4209198596;C:3055507768;G:3382717459;T:3847294849;N:1294858,10,10,28,90,4209198596,3055507768,3382717459,3847294849,1294858,SRX21332626,SRS18578258,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.93428,,0.11629,,0.81014,,0.56014,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25119,SRR25605438,SRX21332625,SRS18578257,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep2,GSM7702832,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702832,GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq,GSM7702832 r1,GSM7702832,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_pos_pos_S1_L001_I1_001.fastq.gz 1907_pos_pos_S1_L001_I2_001.fastq.gz 1907_pos_pos_S1_L001_R1_001.fastq.gz 1907_pos_pos_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,25141955454.0,182188083.0,GSM7702832 r1,0:10 1:10 2:28 3:90,A:4942067104;C:3446689328;G:3778138998;T:4227670796;N:2361244,10,10,28,90,4942067104,3446689328,3778138998,4227670796,2361244,SRX21332625,SRS18578257,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.90803,,0.11273,,0.81872,,0.54345,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25120,SRR25605439,SRX21332625,SRS18578257,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep2,GSM7702832,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702832,GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq,GSM7702832 r1,GSM7702832,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_pos_pos_S1_L002_R2_001.fastq.gz 1907_pos_pos_S1_L002_R1_001.fastq.gz 1907_pos_pos_S1_L002_I2_001.fastq.gz 1907_pos_pos_S1_L002_I1_001.fastq.gz,fastq fastq fastq fastq,25433730786.0,184302397.0,GSM7702832 r2,0:10 1:10 2:28 3:90,A:4980326106;C:3488986366;G:3842594871;T:4275245265;N:63122,10,10,28,90,4980326106,3488986366,3842594871,4275245265,63122,SRX21332625,SRS18578257,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.91035,,0.11175,,0.82016,,0.52814,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25121,SRR25822226,SRX21332625,SRS18578257,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep2,GSM7702832,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702832,GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq,GSM7702832 r1,GSM7702832,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_pos_pos_S1_L001_R2_002.fastq.gz 1907_pos_pos_S1_L001_R1_002.fastq.gz 1907_pos_pos_S1_L001_I2_002.fastq.gz 1907_pos_pos_S1_L001_I1_002.fastq.gz,fastq fastq fastq fastq,24834656088.0,179961276.0,GSM7702832 r3,0:10 1:10 2:28 3:90,A:4878672093;C:3403443000;G:3732878174;T:4180051888;N:1469685,10,10,28,90,4878672093,3403443000,3732878174,4180051888,1469685,SRX21332625,SRS18578257,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.90776,,0.11325,,0.81852,,0.54011,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25122,SRR25822227,SRX21332625,SRS18578257,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep2,GSM7702832,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702832,GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq,GSM7702832 r1,GSM7702832,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_pos_pos_S1_L002_I1_002.fastq.gz 1907_pos_pos_S1_L002_I2_002.fastq.gz 1907_pos_pos_S1_L002_R1_002.fastq.gz 1907_pos_pos_S1_L002_R2_002.fastq.gz,fastq fastq fastq fastq,25609437216.0,185575632.0,GSM7702832 r4,0:10 1:10 2:28 3:90,A:5015380345;C:3509305882;G:3867598814;T:4308011415;N:1510424,10,10,28,90,5015380345,3509305882,3867598814,4308011415,1510424,SRX21332625,SRS18578257,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.90907,,0.11192,,0.81994,,0.50902,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
76372,SRR24954201,SRX20712237,SRS18004425,SRP444513,PRJNA981358,Danio rerio Genome sequencing and assembly,PRJNA981358,Whole Genome Sequencing,To explore the source of Csf1a and Csf1b in embryonic zebrafish  we carried out a single cell RNA sequencing scRNA seq. We collected the trunks from 28 hpf embryos and performed 10X Genomics scRNA seq.,,,This sample contained cells isolated from trunks of 40 zebrafish embryos at 28hpf.,Cells isolated from trunks of wildtype danio rerio at 28hpf,WT 1,,strain:ABSR|dev stage:28 hpf date:2019 11 18|geo loc name:China: Guangzhou|sex:not determined|tissue:Trunk|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of 28hpfWT trunk,28hpfWT 1,28hpfWT 1,Cellular suspensions were loaded on a 10X Genomics GemCode Single cell instrument that generates single cell Gel Bead In EMlusion GEMs. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3 Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM  primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16nt 10x Barcode  iii a 10nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. R1 were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP444513,,,J1911072-ATGCTCCG_BKDL192544560-1a-AK949_2.fq.gz J1911072-CACTCGGA_BKDL192544560-1a-AK946_1.fq.gz J1911072-CACTCGGA_BKDL192544560-1a-AK946_2.fq.gz J1911072-GCTGAATT_BKDL192544560-1a-AK947_1.fq.gz J1911072-GCTGAATT_BKDL192544560-1a-AK947_2.fq.gz J1911072-TGAAGTAC_BKDL192544560-1a-AK948_1.fq.gz J1911072-TGAAGTAC_BKDL192544560-1a-AK948_2.fq.gz J1911072-ATGCTCCG_BKDL192544560-1a-AK949_1.fq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,144260432400.0,480868108.0,J1911072 ATGCTCCG BKDL192544560 1a AK949 1.fq.gz,0:150 1:150,A:57113710706;C:25903289244;G:24836065109;T:36405707402;N:1659939,150,150,,,57113710706,25903289244,24836065109,36405707402,1659939,SRX20712237,SRS18004425,SRA1657728,South China University of Technology|School of Medicine,South China University of Technology,2,0.0,0.92449,0.0,0.12055,1.0,0.77806,,0.51028,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-06-17,Pharyngula,Embryo,Trunk,Surface Structure
76997,SRR25423053,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L001_I1_001.fastq.gz,fastq,39075288.0,4884411.0,GSM7660980 r1,0:8,A:8072562;C:6862766;G:17416494;T:5849783;N:873683,8,,,,8072562,6862766,17416494,5849783,873683,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
76998,SRR25423054,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L004_I1_001.fastq.gz,fastq,40207464.0,5025933.0,GSM7660980 r10,0:8,A:8353613;C:7111546;G:18405023;T:6056882;N:280400,8,,,,8353613,7111546,18405023,6056882,280400,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
76999,SRR25423055,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L004_R1_001.fastq.gz,fastq,140726124.0,5025933.0,GSM7660980 r11,0:28,A:37863942;C:35273460;G:29075767;T:38479070;N:33885,28,,,,37863942,35273460,29075767,38479070,33885,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00815,,0.00373,,0.98762,,0.37971,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77000,SRR25423056,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L004_R2_001.fastq.gz,fastq,653371290.0,5025933.0,GSM7660980 r12,0:130,A:197652493;C:123117545;G:153788236;T:174856024;N:3956992,130,,,,197652493,123117545,153788236,174856024,3956992,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.88819,,0.26058,,0.79498,,0.51248,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77001,SRR25423057,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L001_R1_001.fastq.gz,fastq,136763508.0,4884411.0,GSM7660980 r2,0:28,A:36700123;C:34378994;G:28311664;T:37342519;N:30208,28,,,,36700123,34378994,28311664,37342519,30208,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00746,,0.00299,,0.98782,,0.33891,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77002,SRR25423058,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L001_R2_001.fastq.gz,fastq,634973430.0,4884411.0,GSM7660980 r3,0:130,A:194231988;C:122172940;G:144200881;T:173659068;N:708553,130,,,,194231988,122172940,144200881,173659068,708553,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.89999,,0.26714,,0.78884,,0.51009,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77003,SRR25423059,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L002_I1_001.fastq.gz,fastq,40874608.0,5109326.0,GSM7660980 r4,0:8,A:8407020;C:7216140;G:18310689;T:6123507;N:817252,8,,,,8407020,7216140,18310689,6123507,817252,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77004,SRR25423060,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L002_R1_001.fastq.gz,fastq,143061128.0,5109326.0,GSM7660980 r5,0:28,A:38454355;C:35931605;G:29585361;T:39031878;N:57929,28,,,,38454355,35931605,29585361,39031878,57929,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00783,,0.00316,,0.98744,,0.37064,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77005,SRR25423061,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L002_R2_001.fastq.gz,fastq,664212380.0,5109326.0,GSM7660980 r6,0:130,A:201730540;C:125762436;G:157718531;T:178360911;N:639962,130,,,,201730540,125762436,157718531,178360911,639962,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.88361,,0.26162,,0.79529,,0.50582,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77006,SRR25423062,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L003_I1_001.fastq.gz,fastq,38381576.0,4797697.0,GSM7660980 r7,0:8,A:8075384;C:6797029;G:17490080;T:5805523;N:213560,8,,,,8075384,6797029,17490080,5805523,213560,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77007,SRR25423063,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L003_R1_001.fastq.gz,fastq,134335516.0,4797697.0,GSM7660980 r8,0:28,A:36087906;C:33767454;G:27805596;T:36644298;N:30262,28,,,,36087906,33767454,27805596,36644298,30262,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00769,,0.00317,,0.98729,,0.35107,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77008,SRR25423064,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L003_R2_001.fastq.gz,fastq,623700610.0,4797697.0,GSM7660980 r9,0:130,A:190543769;C:119560339;G:140982942;T:169663923;N:2949637,130,,,,190543769,119560339,140982942,169663923,2949637,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.89981,,0.26806,,0.79026,,0.51173,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77009,SRR25423065,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L001_I1_001.fastq.gz,fastq,41579560.0,5197445.0,GSM7660979 r1,0:8,A:9428308;C:7309725;G:17762022;T:6829664;N:249841,8,,,,9428308,7309725,17762022,6829664,249841,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77010,SRR25423066,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L004_I1_001.fastq.gz,fastq,44075624.0,5509453.0,GSM7660979 r10,0:8,A:9834086;C:7713037;G:19303314;T:7170073;N:55114,8,,,,9834086,7713037,19303314,7170073,55114,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77011,SRR25423067,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L004_R1_001.fastq.gz,fastq,154264684.0,5509453.0,GSM7660979 r11,0:28,A:41220569;C:38745415;G:32338250;T:41944588;N:15862,28,,,,41220569,38745415,32338250,41944588,15862,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00988,,0.00473,,0.98632,,0.39018,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77012,SRR25423068,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L004_R2_001.fastq.gz,fastq,716228890.0,5509453.0,GSM7660979 r12,0:130,A:218476823;C:134111218;G:167891935;T:195631787;N:117127,130,,,,218476823,134111218,167891935,195631787,117127,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.88562,,0.27256,,0.79297,,0.51067,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77013,SRR25423069,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L001_R1_001.fastq.gz,fastq,145528460.0,5197445.0,GSM7660979 r2,0:28,A:38963827;C:36550891;G:30408548;T:39584512;N:20682,28,,,,38963827,36550891,30408548,39584512,20682,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00936,,0.00443,,0.98675,,0.35245,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77014,SRR25423070,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L001_R2_001.fastq.gz,fastq,675667850.0,5197445.0,GSM7660979 r3,0:130,A:208215940;C:128013993;G:151798676;T:187487780;N:151461,130,,,,208215940,128013993,151798676,187487780,151461,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.89748,,0.27631,,0.79064,,0.49734,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77015,SRR25423071,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L002_I1_001.fastq.gz,fastq,45134216.0,5641777.0,GSM7660979 r4,0:8,A:10035142;C:7986132;G:19502502;T:7387873;N:222567,8,,,,10035142,7986132,19502502,7387873,222567,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77016,SRR25423072,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L002_R1_001.fastq.gz,fastq,157969756.0,5641777.0,GSM7660979 r5,0:28,A:42059394;C:39433356;G:33728111;T:42718219;N:30676,28,,,,42059394,39433356,33728111,42718219,30676,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0132,,0.00877,,0.98829,,0.34149,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77017,SRR25423073,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L002_R2_001.fastq.gz,fastq,733431010.0,5641777.0,GSM7660979 r6,0:130,A:222497848;C:136467931;G:175111806;T:199206848;N:146577,130,,,,222497848,136467931,175111806,199206848,146577,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.8786,,0.26704,,0.79433,,0.51215,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77018,SRR25423074,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L003_I1_001.fastq.gz,fastq,41837504.0,5229688.0,GSM7660979 r7,0:8,A:9528062;C:7341028;G:18072427;T:6806346;N:89641,8,,,,9528062,7341028,18072427,6806346,89641,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77019,SRR25423075,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L003_R1_001.fastq.gz,fastq,146431264.0,5229688.0,GSM7660979 r8,0:28,A:39246118;C:36825633;G:30475523;T:39867658;N:16332,28,,,,39246118,36825633,30475523,39867658,16332,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00821,,0.00344,,0.98703,,0.36121,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77020,SRR25423076,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L003_R2_001.fastq.gz,fastq,679859440.0,5229688.0,GSM7660979 r9,0:130,A:210099119;C:129100730;G:151835050;T:188699403;N:125138,130,,,,210099119,129100730,151835050,188699403,125138,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.89817,,0.27686,,0.78839,,0.50029,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77021,SRR25423077,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L001_I1_001.fastq.gz,fastq,41558296.0,5194787.0,GSM7660978 r1,0:8,A:8653956;C:7501606;G:18389913;T:6889579;N:123242,8,,,,8653956,7501606,18389913,6889579,123242,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77022,SRR25423078,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L004_I1_001.fastq.gz,fastq,44153920.0,5519240.0,GSM7660978 r10,0:8,A:9112539;C:7989581;G:19589834;T:7272691;N:189275,8,,,,9112539,7989581,19589834,7272691,189275,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77023,SRR25423079,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L004_R1_001.fastq.gz,fastq,154538720.0,5519240.0,GSM7660978 r11,0:28,A:41768269;C:38565549;G:31995336;T:42189478;N:20088,28,,,,41768269,38565549,31995336,42189478,20088,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00832,,0.00399,,0.98802,,0.387,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77024,SRR25423080,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L004_R2_001.fastq.gz,fastq,717501200.0,5519240.0,GSM7660978 r12,0:130,A:223425289;C:128869376;G:157867154;T:204364748;N:2974633,130,,,,223425289,128869376,157867154,204364748,2974633,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86456,,0.33873,,0.80712,,0.51252,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77025,SRR25423081,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L001_R1_001.fastq.gz,fastq,145454036.0,5194787.0,GSM7660978 r2,0:28,A:39325327;C:36299242;G:30079706;T:39733166;N:16595,28,,,,39325327,36299242,30079706,39733166,16595,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00777,,0.00372,,0.98912,,0.34306,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77026,SRR25423082,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L001_R2_001.fastq.gz,fastq,675322310.0,5194787.0,GSM7660978 r3,0:130,A:211915718;C:123090340;G:143012180;T:195734602;N:1569470,130,,,,211915718,123090340,143012180,195734602,1569470,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87849,,0.34767,,0.80056,,0.50735,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77027,SRR25423083,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L002_I1_001.fastq.gz,fastq,44049120.0,5506140.0,GSM7660978 r4,0:8,A:8944566;C:7961128;G:19746021;T:7226687;N:170718,8,,,,8944566,7961128,19746021,7226687,170718,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77028,SRR25423084,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L002_R1_001.fastq.gz,fastq,154171920.0,5506140.0,GSM7660978 r5,0:28,A:41607797;C:38479559;G:31947188;T:42108428;N:28948,28,,,,41607797,38479559,31947188,42108428,28948,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0082,,0.0037,,0.98764,,0.36041,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77029,SRR25423085,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L002_R2_001.fastq.gz,fastq,715798200.0,5506140.0,GSM7660978 r6,0:130,A:220199429;C:127429364;G:164452265;T:202077008;N:1640134,130,,,,220199429,127429364,164452265,202077008,1640134,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86141,,0.34092,,0.80892,,0.51636,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77030,SRR25423086,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L003_I1_001.fastq.gz,fastq,41701648.0,5212706.0,GSM7660978 r7,0:8,A:8699211;C:7482837;G:18518090;T:6841716;N:159794,8,,,,8699211,7482837,18518090,6841716,159794,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77031,SRR25423087,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L003_R1_001.fastq.gz,fastq,145955768.0,5212706.0,GSM7660978 r8,0:28,A:39432715;C:36411478;G:30250823;T:39840040;N:20712,28,,,,39432715,36411478,30250823,39840040,20712,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00842,,0.00384,,0.98746,,0.37644,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77032,SRR25423088,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L003_R2_001.fastq.gz,fastq,677651780.0,5212706.0,GSM7660978 r9,0:130,A:212834801;C:123716124;G:143169759;T:196419860;N:1511236,130,,,,212834801,123716124,143169759,196419860,1511236,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87783,,0.34587,,0.80004,,0.50737,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77033,SRR25423089,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L001_I1_001.fastq.gz,fastq,28230536.0,3528817.0,GSM7660977 r1,0:8,A:5846993;C:4500398;G:13413679;T:4284440;N:185026,8,,,,5846993,4500398,13413679,4284440,185026,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77034,SRR25423090,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L004_I1_001.fastq.gz,fastq,29841512.0,3730189.0,GSM7660977 r10,0:8,A:5996183;C:4745155;G:14573475;T:4491992;N:34707,8,,,,5996183,4745155,14573475,4491992,34707,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77035,SRR25423091,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L004_R1_001.fastq.gz,fastq,104445292.0,3730189.0,GSM7660977 r11,0:28,A:27569833;C:25852975;G:23011555;T:27996654;N:14275,28,,,,27569833,25852975,23011555,27996654,14275,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.028,,0.02215,,0.98616,,0.37606,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77036,SRR25423092,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L004_R2_001.fastq.gz,fastq,484924570.0,3730189.0,GSM7660977 r12,0:130,A:146960114;C:85137895;G:117712649;T:135019012;N:94900,130,,,,146960114,85137895,117712649,135019012,94900,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.8426,,0.343,,0.80904,,0.51553,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77037,SRR25423093,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L001_R1_001.fastq.gz,fastq,98806876.0,3528817.0,GSM7660977 r2,0:28,A:26486103;C:24902412;G:20399917;T:26995262;N:23182,28,,,,26486103,24902412,20399917,26995262,23182,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00972,,0.00476,,0.9867,,0.37988,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77038,SRR25423094,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L001_R2_001.fastq.gz,fastq,458746210.0,3528817.0,GSM7660977 r3,0:130,A:142756416;C:83435608;G:99381174;T:132821566;N:351446,130,,,,142756416,83435608,99381174,132821566,351446,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87492,,0.35523,,0.8005,,0.51302,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77039,SRR25423095,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L002_I1_001.fastq.gz,fastq,29813552.0,3726694.0,GSM7660977 r4,0:8,A:6023894;C:4790724;G:14323297;T:4511397;N:164240,8,,,,6023894,4790724,14323297,4511397,164240,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77040,SRR25423096,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L002_R1_001.fastq.gz,fastq,104347432.0,3726694.0,GSM7660977 r5,0:28,A:27972757;C:26292261;G:21550202;T:28495595;N:36617,28,,,,27972757,26292261,21550202,28495595,36617,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00972,,0.0048,,0.98642,,0.38768,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77041,SRR25423097,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L002_R2_001.fastq.gz,fastq,484470220.0,3726694.0,GSM7660977 r6,0:130,A:148967159;C:86626052;G:111069442;T:137592736;N:214831,130,,,,148967159,86626052,111069442,137592736,214831,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.8627,,0.3511,,0.80537,,0.51342,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77042,SRR25423098,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L003_I1_001.fastq.gz,fastq,27884800.0,3485600.0,GSM7660977 r7,0:8,A:5814876;C:4428196;G:13359658;T:4213922;N:68148,8,,,,5814876,4428196,13359658,4213922,68148,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77043,SRR25423099,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L003_R1_001.fastq.gz,fastq,97596800.0,3485600.0,GSM7660977 r8,0:28,A:26153650;C:24561941;G:20253854;T:26610923;N:16432,28,,,,26153650,24561941,20253854,26610923,16432,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01092,,0.00601,,0.9865,,0.37684,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77044,SRR25423100,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L003_R2_001.fastq.gz,fastq,453128000.0,3485600.0,GSM7660977 r9,0:130,A:140968028;C:82271283;G:99033183;T:130715848;N:139658,130,,,,140968028,82271283,99033183,130715848,139658,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87275,,0.3559,,0.80182,,0.51746,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77045,SRR25423101,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L001_I1_001.fastq.gz,fastq,29787544.0,3723443.0,GSM7660976 r1,0:8,A:6291781;C:4754023;G:14140176;T:4509077;N:92487,8,,,,6291781,4754023,14140176,4509077,92487,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77046,SRR25423102,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L004_I1_001.fastq.gz,fastq,31294328.0,3911791.0,GSM7660976 r10,0:8,A:6592572;C:5083904;G:14754028;T:4819225;N:44599,8,,,,6592572,5083904,14754028,4819225,44599,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77047,SRR25423103,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L004_R1_001.fastq.gz,fastq,109530148.0,3911791.0,GSM7660976 r11,0:28,A:29597133;C:27430169;G:22526281;T:29958507;N:18058,28,,,,29597133,27430169,22526281,29958507,18058,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00894,,0.00415,,0.98735,,0.40096,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77048,SRR25423104,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L004_R2_001.fastq.gz,fastq,508532830.0,3911791.0,GSM7660976 r12,0:130,A:159207324;C:90927654;G:114226247;T:144088377;N:83228,130,,,,159207324,90927654,114226247,144088377,83228,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86494,,0.35089,,0.80965,,0.50948,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77049,SRR25423105,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L001_R1_001.fastq.gz,fastq,104256404.0,3723443.0,GSM7660976 r2,0:28,A:28240149;C:26091346;G:21397649;T:28513954;N:13306,28,,,,28240149,26091346,21397649,28513954,13306,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00927,,0.00429,,0.98701,,0.38362,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System