{"database": "metadata", "table": "run_metadata", "rows": [[28191, "SRR26209727", "SRX21920647", "SRS19005166", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates  yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family  FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed  two pathways often dysregulated in disease.  Insights into gene function can often be gained by studying the roles they play during development  and here we report the generation of fam83f knock out fam83f /  zebrafish  which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos  and that fam83f /  embryos hatch earlier than WT counterparts  despite developing at a comparable temporal rate. We demonstrate that fam83f /  embryos are more sensitive to ionizing radiation than WT embryos  a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways  particularly autophagy  which is a crucial component of the DNA damage response. Finally  we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells  and that this localization is dependent upon a C' terminal signal sequence.  The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes  resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa /  zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa /  K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2.  Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa /  mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "un t1 K2 2", "GSM7812996", null, "source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing", "un t1 K2 2", "Cutadapt  1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files", "whole embryo", "Embryos were exposed to gamma IR of 20 Gy at xxx hpf", "Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina  then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms", "Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density \u22dc  50 embryos", "tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un", "GSM7812996", "GSM7812996: un t1 K2 2; Danio rerio; RNA Seq", "GSM7812996 r1", "GSM7812996", "1", "Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina  then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "loader:fastq load.py", "JON686A8_S23_L007_R1_001.fastq.gz", "fastq", 625918816.0, 6197216.0, "GSM7812996 r4", "0:101", "A:157368110;C:149165182;G:141695477;T:177678522;N:11525", 101, null, null, null, 157368110, 149165182, 141695477, 177678522, 11525, "SRX21920647", "SRS19005166", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.9397, null, 0.07494, null, 0.69098, null, 0.47166, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"]], "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": ["28191"], "units": {}, "query_ms": 9.342526012915187}