{"database": "metadata", "table": "run_metadata", "rows": [[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"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["77055"], "units": {}, "query_ms": 8.080575993517414}