{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"10x\" and tissue_curation = \"Brain\"", "rows": [[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. 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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. 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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. 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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. 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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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane3 & lane4", "GSM7660980", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00299, null, 0.98782, null, 0.33891, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane3 & lane4", "GSM7660980", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.26714, null, 0.78884, null, 0.51009, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane3 & lane4", "GSM7660980", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane3 & lane4", "GSM7660980", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00316, null, 0.98744, null, 0.37064, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane3 & lane4", "GSM7660980", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.26162, null, 0.79529, null, 0.50582, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane3 & lane4", "GSM7660980", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane3 & lane4", "GSM7660980", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00317, null, 0.98729, null, 0.35107, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane3 & lane4", "GSM7660980", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.26806, null, 0.79026, null, 0.51173, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00473, null, 0.98632, null, 0.39018, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.27256, null, 0.79297, null, 0.51067, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00443, null, 0.98675, null, 0.35245, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.27631, null, 0.79064, null, 0.49734, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00877, null, 0.98829, null, 0.34149, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.26704, null, 0.79433, null, 0.51215, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00344, null, 0.98703, null, 0.36121, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "WT s1026 rep1 lane1 & lane2", "GSM7660979", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.27686, null, 0.78839, null, 0.50029, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00399, null, 0.98802, null, 0.387, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.33873, null, 0.80712, null, 0.51252, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00372, null, 0.98912, null, 0.34306, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.34767, null, 0.80056, null, 0.50735, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0037, null, 0.98764, null, 0.36041, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.34092, null, 0.80892, null, 0.51636, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00384, null, 0.98746, null, 0.37644, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep4 lane1 & lane2", "GSM7660978", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.34587, null, 0.80004, null, 0.50737, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.02215, null, 0.98616, null, 0.37606, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.343, null, 0.80904, null, 0.51553, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00476, null, 0.9867, null, 0.37988, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.35523, null, 0.8005, null, 0.51302, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0048, null, 0.98642, null, 0.38768, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.3511, null, 0.80537, null, 0.51342, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00601, null, 0.9865, null, 0.37684, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane3 & lane4", "GSM7660977", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.3559, null, 0.80182, null, 0.51746, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00415, null, 0.98735, null, 0.40096, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.35089, null, 0.80965, null, 0.50948, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00429, null, 0.98701, null, 0.38362, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.3547, null, 0.80397, null, 0.51066, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0104, null, 0.98768, null, 0.39479, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.34647, null, 0.80915, null, 0.51666, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00455, null, 0.98727, null, 0.38461, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep3 lane1 & lane2", "GSM7660976", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.35537, null, 0.80578, null, 0.51406, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00484, null, 0.98269, null, 0.39781, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.35594, null, 0.79644, null, 0.48808, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00515, null, 0.98259, null, 0.38268, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.36363, null, 0.79368, null, 0.49204, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00667, null, 0.98131, null, 0.38461, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.35745, null, 0.79819, null, 0.48731, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00502, null, 0.98263, null, 0.34829, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep2 lane1 & lane2", "GSM7660975", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.36563, null, 0.79464, null, 0.49983, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00445, null, 0.98468, null, 0.34528, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.34597, null, 0.8031, null, 0.50312, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00474, null, 0.98427, null, 0.32676, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.35109, null, 0.80119, null, 0.5131, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00436, null, 0.98397, null, 0.34301, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.34572, null, 0.80474, null, 0.50989, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00515, null, 0.98512, null, 0.34082, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "lakritz HGn12C rep1 lane1 & lane2", "GSM7660974", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.3512, null, 0.8015, null, 0.50656, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00389, null, 0.98559, null, 0.36606, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.32497, null, 0.80588, null, 0.51279, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00455, null, 0.98695, null, 0.39649, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.32904, null, 0.80127, null, 0.508, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00792, null, 0.98581, null, 0.38261, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.3214, null, 0.8089, null, 0.51731, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.00469, null, 0.98614, null, 0.37162, null, 28, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep3 lane1 & lane2", "GSM7660973", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.33026, null, 0.80089, null, 0.51535, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep2 lane1 & lane2", "GSM7660972", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:37758715", null, "Related WT HGn12C rep2 lane1 & lane2", "GSM7660972", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP451428", null, null, "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, null, null, null, 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, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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. 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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.", null, "pubmed:37758715", null, "Related WT HGn12C rep2 lane1 & lane2", "GSM7660972", null, "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", null, "Cell dissociation 10X genomics", null, "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", null, 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