run_metadata: 28130

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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
28130	SRR26209664	SRX21920659	SRS19005178	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		pubmed:39437839		unDMSO t1 K2 3	GSM7812988		source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K2 3	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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO	GSM7812988	GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq	GSM7812988 r1	GSM7812988	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP463749		loader:fastq load.py	JON686A36_S54_L007_R1_001.fastq.gz	fastq	596645683.0	5907383.0	GSM7812988 r3	0:101	A:153131508;C:143126741;G:134745614;T:165635953;N:5867	101				153131508	143126741	134745614	165635953	5867	SRX21920659	SRS19005178	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94156		0.07795		0.69751		0.4833		101		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	unknown	bulk	bulk	bulk		United States	2023-09-28	Undetermined	Embryo	Whole Organism	All anatomical structures