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 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 77050,SRR25423106,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_R2_001.fastq.gz,fastq,484047590.0,3723443.0,GSM7660976 r3,0:130,A:153076719;C:87852215;G:103323528;T:139733266;N:61862,130,,,,153076719,87852215,103323528,139733266,61862,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87385,,0.3547,,0.80397,,0.51066,,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 77051,SRR25423107,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_L002_I1_001.fastq.gz,fastq,31052016.0,3881502.0,GSM7660976 r4,0:8,A:6427800;C:4967419;G:14857276;T:4682418;N:117103,8,,,,6427800,4967419,14857276,4682418,117103,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 77052,SRR25423108,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_L002_R1_001.fastq.gz,fastq,108682056.0,3881502.0,GSM7660976 r5,0:28,A:29226161;C:27023100;G:22866742;T:29528967;N:37086,28,,,,29226161,27023100,22866742,29528967,37086,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01532,,0.0104,,0.98768,,0.39479,,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 77053,SRR25423109,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_L002_R2_001.fastq.gz,fastq,504595260.0,3881502.0,GSM7660976 r6,0:130,A:156874723;C:89614357;G:115903779;T:142154131;N:48270,130,,,,156874723,89614357,115903779,142154131,48270,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.85688,,0.34647,,0.80915,,0.51666,,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 77054,SRR25423110,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_L003_I1_001.fastq.gz,fastq,29923968.0,3740496.0,GSM7660976 r7,0:8,A:6366100;C:4759295;G:14243169;T:4506312;N:49092,8,,,,6366100,4759295,14243169,4506312,49092,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 77055,SRR25423111,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_L003_R1_001.fastq.gz,fastq,104733888.0,3740496.0,GSM7660976 r8,0:28,A:28415676;C:26199206;G:21498271;T:28607903;N:12832,28,,,,28415676,26199206,21498271,28607903,12832,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0094,,0.00455,,0.98727,,0.38461,,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 77056,SRR25423112,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_L003_R2_001.fastq.gz,fastq,486264480.0,3740496.0,GSM7660976 r9,0:130,A:154026351;C:88159638;G:103993801;T:140006983;N:77707,130,,,,154026351,88159638,103993801,140006983,77707,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.8762,,0.35537,,0.80578,,0.51406,,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 77057,SRR25423113,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L001_I1_001.fastq.gz,fastq,31103088.0,3887886.0,GSM7660975 r1,0:8,A:6361484;C:4897580;G:14297020;T:4689154;N:857850,8,,,,6361484,4897580,14297020,4689154,857850,SRX21157889,SRS18420142,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 77058,SRR25423114,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L004_I1_001.fastq.gz,fastq,32085984.0,4010748.0,GSM7660975 r10,0:8,A:6540927;C:5122399;G:15367165;T:4844195;N:211298,8,,,,6540927,5122399,15367165,4844195,211298,SRX21157889,SRS18420142,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 77059,SRR25423115,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L004_R1_001.fastq.gz,fastq,112300944.0,4010748.0,GSM7660975 r11,0:28,A:29834480;C:28332816;G:23373084;T:30727974;N:32590,28,,,,29834480,28332816,23373084,30727974,32590,SRX21157889,SRS18420142,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01154,,0.00484,,0.98269,,0.39781,,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 77060,SRR25423116,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L004_R2_001.fastq.gz,fastq,521397240.0,4010748.0,GSM7660975 r12,0:130,A:160244624;C:93004147;G:119150426;T:146963140;N:2034903,130,,,,160244624,93004147,119150426,146963140,2034903,SRX21157889,SRS18420142,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86293,,0.35594,,0.79644,,0.48808,,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 77061,SRR25423117,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L001_R1_001.fastq.gz,fastq,108860808.0,3887886.0,GSM7660975 r2,0:28,A:28991208;C:27461535;G:22581250;T:29801436;N:25379,28,,,,28991208,27461535,22581250,29801436,25379,SRX21157889,SRS18420142,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01209,,0.00515,,0.98259,,0.38268,,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 77062,SRR25423118,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L001_R2_001.fastq.gz,fastq,505425180.0,3887886.0,GSM7660975 r3,0:130,A:157391291;C:91583767;G:110558946;T:145340796;N:550380,130,,,,157391291,91583767,110558946,145340796,550380,SRX21157889,SRS18420142,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87423,,0.36363,,0.79368,,0.49204,,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 77063,SRR25423119,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L002_I1_001.fastq.gz,fastq,33332576.0,4166572.0,GSM7660975 r4,0:8,A:6700555;C:5338889;G:15406096;T:5057205;N:829831,8,,,,6700555,5338889,15406096,5057205,829831,SRX21157889,SRS18420142,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 77064,SRR25423120,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L002_R1_001.fastq.gz,fastq,116664016.0,4166572.0,GSM7660975 r5,0:28,A:30967374;C:29348878;G:24439236;T:31856457;N:52071,28,,,,30967374,29348878,24439236,31856457,52071,SRX21157889,SRS18420142,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0139,,0.00667,,0.98131,,0.38461,,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 77065,SRR25423121,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L002_R2_001.fastq.gz,fastq,541654360.0,4166572.0,GSM7660975 r6,0:130,A:166741502;C:96581544;G:124638465;T:152958527;N:734322,130,,,,166741502,96581544,124638465,152958527,734322,SRX21157889,SRS18420142,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86168,,0.35745,,0.79819,,0.48731,,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 77066,SRR25423122,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L003_I1_001.fastq.gz,fastq,30432944.0,3804118.0,GSM7660975 r7,0:8,A:6332328;C:4852182;G:14467825;T:4603825;N:176784,8,,,,6332328,4852182,14467825,4603825,176784,SRX21157889,SRS18420142,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 77067,SRR25423123,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L003_R1_001.fastq.gz,fastq,106515304.0,3804118.0,GSM7660975 r8,0:28,A:28360844;C:26884367;G:22106125;T:29141204;N:22764,28,,,,28360844,26884367,22106125,29141204,22764,SRX21157889,SRS18420142,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01176,,0.00502,,0.98263,,0.34829,,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 77068,SRR25423124,SRX21157889,SRS18420142,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 rep2 lane1 & lane2,GSM7660975,,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 rep2 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,GSM7660975,GSM7660975: lakritz HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660975 r1,GSM7660975,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p151_S0_L003_R2_001.fastq.gz,fastq,494535340.0,3804118.0,GSM7660975 r9,0:130,A:154062076;C:89642475;G:107902132;T:141894552;N:1034105,130,,,,154062076,89642475,107902132,141894552,1034105,SRX21157889,SRS18420142,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87641,,0.36563,,0.79464,,0.49983,,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 77069,SRR25423125,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L001_I1_001.fastq.gz,fastq,42003328.0,5250416.0,GSM7660974 r1,0:8,A:7962034;C:7171244;G:19647119;T:6870161;N:352770,8,,,,7962034,7171244,19647119,6870161,352770,SRX21157888,SRS18420141,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 77070,SRR25423126,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L004_I1_001.fastq.gz,fastq,43524912.0,5440614.0,GSM7660974 r10,0:8,A:8062855;C:7431505;G:20934461;T:7027375;N:68716,8,,,,8062855,7431505,20934461,7027375,68716,SRX21157888,SRS18420141,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 77071,SRR25423127,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L004_R1_001.fastq.gz,fastq,152337192.0,5440614.0,GSM7660974 r11,0:28,A:40507321;C:38566030;G:31491352;T:41746664;N:25825,28,,,,40507321,38566030,31491352,41746664,25825,SRX21157888,SRS18420141,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01043,,0.00445,,0.98468,,0.34528,,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 77072,SRR25423128,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L004_R2_001.fastq.gz,fastq,707279820.0,5440614.0,GSM7660974 r12,0:130,A:217464440;C:126346070;G:164255397;T:198542973;N:670940,130,,,,217464440,126346070,164255397,198542973,670940,SRX21157888,SRS18420141,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.85871,,0.34597,,0.8031,,0.50312,,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 77073,SRR25423129,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L001_R1_001.fastq.gz,fastq,147011648.0,5250416.0,GSM7660974 r2,0:28,A:39110458;C:37212994;G:30364131;T:40299317;N:24748,28,,,,39110458,37212994,30364131,40299317,24748,SRX21157888,SRS18420141,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01081,,0.00474,,0.98427,,0.32676,,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 77074,SRR25423130,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L001_R2_001.fastq.gz,fastq,682554080.0,5250416.0,GSM7660974 r3,0:130,A:211991295;C:123694502;G:151573221;T:195142735;N:152327,130,,,,211991295,123694502,151573221,195142735,152327,SRX21157888,SRS18420141,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87171,,0.35109,,0.80119,,0.5131,,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 77075,SRR25423131,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L002_I1_001.fastq.gz,fastq,43782408.0,5472801.0,GSM7660974 r4,0:8,A:8142354;C:7528891;G:20734268;T:7106308;N:270587,8,,,,8142354,7528891,20734268,7106308,270587,SRX21157888,SRS18420141,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 77076,SRR25423132,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L002_R1_001.fastq.gz,fastq,153238428.0,5472801.0,GSM7660974 r5,0:28,A:40803467;C:38782794;G:31623536;T:41994794;N:33837,28,,,,40803467,38782794,31623536,41994794,33837,SRX21157888,SRS18420141,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0106,,0.00436,,0.98397,,0.34301,,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 77077,SRR25423133,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L002_R2_001.fastq.gz,fastq,711464130.0,5472801.0,GSM7660974 r6,0:130,A:218755080;C:126881047;G:165868188;T:199839034;N:120781,130,,,,218755080,126881047,165868188,199839034,120781,SRX21157888,SRS18420141,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.85717,,0.34572,,0.80474,,0.50989,,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 77078,SRR25423134,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L003_I1_001.fastq.gz,fastq,41714136.0,5214267.0,GSM7660974 r7,0:8,A:7914363;C:7095363;G:19829153;T:6799156;N:76101,8,,,,7914363,7095363,19829153,6799156,76101,SRX21157888,SRS18420141,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 77079,SRR25423135,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L003_R1_001.fastq.gz,fastq,145999476.0,5214267.0,GSM7660974 r8,0:28,A:38867665;C:36935651;G:30222768;T:39953898;N:19494,28,,,,38867665,36935651,30222768,39953898,19494,SRX21157888,SRS18420141,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01094,,0.00515,,0.98512,,0.34082,,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 77080,SRR25423136,SRX21157888,SRS18420141,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 rep1 lane1 & lane2,GSM7660974,,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 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:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660974,GSM7660974: lakritz HGn12C rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660974 r1,GSM7660974,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p139_S0_L003_R2_001.fastq.gz,fastq,677854710.0,5214267.0,GSM7660974 r9,0:130,A:210532090;C:122510565;G:151679974;T:192945966;N:186115,130,,,,210532090,122510565,151679974,192945966,186115,SRX21157888,SRS18420141,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.8694,,0.3512,,0.8015,,0.50656,,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 77081,SRR25423137,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L001_I1_001.fastq.gz,fastq,39460552.0,4932569.0,GSM7660973 r1,0:8,A:8953946;C:7543307;G:16155311;T:6017148;N:790840,8,,,,8953946,7543307,16155311,6017148,790840,SRX21157887,SRS18420140,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 77082,SRR25423138,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L004_I1_001.fastq.gz,fastq,39767936.0,4970992.0,GSM7660973 r10,0:8,A:9228151;C:7712019;G:16377386;T:6193534;N:256846,8,,,,9228151,7712019,16377386,6193534,256846,SRX21157887,SRS18420140,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 77083,SRR25423139,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L004_R1_001.fastq.gz,fastq,139187776.0,4970992.0,GSM7660973 r11,0:28,A:37144393;C:34977093;G:29105885;T:37911244;N:49161,28,,,,37144393,34977093,29105885,37911244,49161,SRX21157887,SRS18420140,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00921,,0.00389,,0.98559,,0.36606,,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 77084,SRR25423140,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L004_R2_001.fastq.gz,fastq,646228960.0,4970992.0,GSM7660973 r12,0:130,A:200371263;C:115887836;G:144118739;T:182916634;N:2934488,130,,,,200371263,115887836,144118739,182916634,2934488,SRX21157887,SRS18420140,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87241,,0.32497,,0.80588,,0.51279,,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 77085,SRR25423141,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L001_R1_001.fastq.gz,fastq,138111932.0,4932569.0,GSM7660973 r2,0:28,A:36837367;C:34734568;G:28944374;T:37567298;N:28325,28,,,,36837367,34734568,28944374,37567298,28325,SRX21157887,SRS18420140,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0094,,0.00455,,0.98695,,0.39649,,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 77086,SRR25423142,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L001_R2_001.fastq.gz,fastq,641233970.0,4932569.0,GSM7660973 r3,0:130,A:199564957;C:116766686;G:138047549;T:184396837;N:2457941,130,,,,199564957,116766686,138047549,184396837,2457941,SRX21157887,SRS18420140,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87795,,0.32904,,0.80127,,0.508,,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 77087,SRR25423143,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L002_I1_001.fastq.gz,fastq,41277944.0,5159743.0,GSM7660973 r4,0:8,A:9297061;C:7928277;G:17012800;T:6306461;N:733345,8,,,,9297061,7928277,17012800,6306461,733345,SRX21157887,SRS18420140,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 77088,SRR25423144,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L002_R1_001.fastq.gz,fastq,144472804.0,5159743.0,GSM7660973 r5,0:28,A:38430851;C:36177270;G:30630914;T:39148500;N:85269,28,,,,38430851,36177270,30630914,39148500,85269,SRX21157887,SRS18420140,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01294,,0.00792,,0.98581,,0.38261,,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 77089,SRR25423145,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L002_R2_001.fastq.gz,fastq,670766590.0,5159743.0,GSM7660973 r6,0:130,A:206562105;C:119965701;G:153010845;T:189080532;N:2147407,130,,,,206562105,119965701,153010845,189080532,2147407,SRX21157887,SRS18420140,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86163,,0.3214,,0.8089,,0.51731,,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 77090,SRR25423146,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L003_I1_001.fastq.gz,fastq,38362360.0,4795295.0,GSM7660973 r7,0:8,A:9004404;C:7431779;G:15680123;T:5982786;N:263268,8,,,,9004404,7431779,15680123,5982786,263268,SRX21157887,SRS18420140,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 77091,SRR25423147,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L003_R1_001.fastq.gz,fastq,134268260.0,4795295.0,GSM7660973 r8,0:28,A:35952101;C:33696476;G:28038028;T:36548718;N:32937,28,,,,35952101,33696476,28038028,36548718,32937,SRX21157887,SRS18420140,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00976,,0.00469,,0.98614,,0.37162,,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 77092,SRR25423148,SRX21157887,SRS18420140,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,,Related WT HGn12C rep3 lane1 & lane2,GSM7660973,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT 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:Related WT|treatment:N1,GSM7660973,GSM7660973: Related WT HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660973 r1,GSM7660973,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p201_S0_L003_R2_001.fastq.gz,fastq,623388350.0,4795295.0,GSM7660973 r9,0:130,A:195001360;C:113392375;G:133057487;T:179157144;N:2779984,130,,,,195001360,113392375,133057487,179157144,2779984,SRX21157887,SRS18420140,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.88197,,0.33026,,0.80089,,0.51535,,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 77093,SRR25423149,SRX21157886,SRS18420139,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,,Related WT HGn12C rep2 lane1 & lane2,GSM7660972,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT HGn12C rep2 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:Related WT|treatment:N1,GSM7660972,GSM7660972: Related WT HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660972 r1,GSM7660972,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p200_S0_L001_I1_001.fastq.gz,fastq,39673400.0,4959175.0,GSM7660972 r1,0:8,A:8405683;C:7062796;G:17186387;T:6122085;N:896449,8,,,,8405683,7062796,17186387,6122085,896449,SRX21157886,SRS18420139,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 77094,SRR25423150,SRX21157886,SRS18420139,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,,Related WT HGn12C rep2 lane1 & lane2,GSM7660972,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT HGn12C rep2 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:Related WT|treatment:N1,GSM7660972,GSM7660972: Related WT HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660972 r1,GSM7660972,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p200_S0_L004_I1_001.fastq.gz,fastq,40367936.0,5045992.0,GSM7660972 r10,0:8,A:8513253;C:7220634;G:18142296;T:6233947;N:257806,8,,,,8513253,7220634,18142296,6233947,257806,SRX21157886,SRS18420139,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 77095,SRR25423151,SRX21157886,SRS18420139,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,,Related WT HGn12C rep2 lane1 & lane2,GSM7660972,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT HGn12C rep2 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:Related WT|treatment:N1,GSM7660972,GSM7660972: Related WT HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660972 r1,GSM7660972,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p200_S0_L004_R1_001.fastq.gz,fastq,141287776.0,5045992.0,GSM7660972 r11,0:28,A:37285211;C:34411133;G:32152644;T:37401843;N:36945,28,,,,37285211,34411133,32152644,37401843,36945,SRX21157886,SRS18420139,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01022,,0.00833,,0.99419,,0.38888,,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 77096,SRR25423152,SRX21157886,SRS18420139,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,,Related WT HGn12C rep2 lane1 & lane2,GSM7660972,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:Related WT|treatment:N1|geo loc name:missing|collection date:missing,Related WT HGn12C rep2 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:Related WT|treatment:N1,GSM7660972,GSM7660972: Related WT HGn12C rep2 lane1 & lane2; Danio rerio; RNA Seq,GSM7660972 r1,GSM7660972,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p200_S0_L004_R2_001.fastq.gz,fastq,655978960.0,5045992.0,GSM7660972 r12,0:130,A:197189718;C:111672384;G:145391061;T:186355392;N:15370405,130,,,,197189718,111672384,145391061,186355392,15370405,SRX21157886,SRS18420139,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.84165,,0.3016,,0.81217,,0.49592,,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