{"database": "metadata", "table": "run_metadata", "rows": [[34265, "SRR31620790", "SRX26985239", "SRS23451897", "SRP549631", "PRJNA1194578", "Tet proteins regulate differentiation potential across retinal cell types", "GSE283588", "Transcriptome Analysis", "Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis\u2013revealing that Tet nulltet2 / ;tet3 /  zebrafish exhibit extensive retinal defects. Here  we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 /  phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 /  retinae including delayed specification of several retinal cell types  reduced maturity across late stage tet2 / ;tet3 /  cones  expansions of immature subpopulations of both horizontal and bipolar cells  and altered biases of bipolar cell subtype fates at late differentiation stages. Together  these data support Tet proteins as regulators of cell specification  lineage fate commitment  and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72  and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 /  retinae. Dissociated cells were analyzed via scRNAseq", null, "pubmed:39713311;pubmed:40140485", null, "36hpf dmut replicate 1", "GSM8666792", null, "source name:eye|tissue:eye|age:36|genotype:tet2 / tet3 / |geo loc name:missing|collection date:missing", "36hpf dmut replicate 1", "Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction  normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files", "eye", null, "Whole sibCTL and tet2 / tet3 /  eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin  with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment  in 2 separate wells  sibCTL and  tet2 / tet3 /   dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS.  Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads  and PCR amplified. post PCR amplification  cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "tissue:eye|age:36|genotype:tet2 / tet3 / ", "GSM8666792", "GSM8666792: 36hpf dmut replicate 1; Danio rerio; RNA Seq", "GSM8666792 r1", "GSM8666792", "1", "Whole sibCTL and tet2 / tet3 /  eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin  with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment  in 2 separate wells  sibCTL and  tet2 / tet3 /   dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS.  Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads  and PCR amplified. post PCR amplification  cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP549631", null, null, "36_1DMUT_LIBRARY_GRO2455A6_S8_L001_R1_001.fastq.gz 36_1DMUT_LIBRARY_GRO2455A6_S8_L001_R2_001.fastq.gz", "fastq fastq", 59960371084.0, 508138738.0, "GSM8666792 r1", "0:28 1:90", "A:16529389286;C:13737763948;G:14793638663;T:14896546895;N:3032292", 28, 90, null, null, 16529389286, 13737763948, 14793638663, 14896546895, 3032292, "SRX26985239", "SRS23451897", "SRA2028272", "Gross, Ophthalmology, University of Pittsburgh", "Gross, Ophthalmology, University of Pittsburgh", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-05", "Multi-stage", "Multi-stage", "Eye", "Sensory 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": ["34265"], "units": {}, "query_ms": 9.37805699504679}