metadata: run_metadata: 1,586 rows where experiment.library_selection = "cDNA", technology = "bulk" and tissue_curation

1,586 rows where experiment.library_selection = "cDNA", technology = "bulk" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
24652	24652	SRR25487068	SRX21218619	SRS18475798	SRP452670	PRJNA1000968	CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo	GSE239788	Transcriptome Analysis	Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.		pubmed:38114601	nexn / biological replicate 2	GSM7673294	source name:whole organism\|tissue:whole organism\|genotype:nexn knockout\|geo loc name:missing\|collection date:missing	nexn / biological replicate 2	Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value	whole organism		RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics		tissue:whole organism\|genotype:nexn knockout	GSM7673294	GSM7673294: nexn / biological replicate 2; Danio rerio; RNA Seq	GSM7673294 r1	GSM7673294	1	RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP452670	loader:fastq load.py	NG-33220_nexn_E2_mut3_lib700540_10254_1_2.fastq.gz NG-33220_nexn_E2_mut3_lib700540_10254_1_1.fastq.gz	fastq fastq	12821226686.0	42454393.0	GSM7673294 r1	0:151 1:151	A:3460123169;C:2958819646;G:3023309404;T:3378893399;N:81068	151	151	3460123169	2958819646	3023309404	3378893399	81068	SRX21218619	SRS18475798	SRA1684694	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	2	0.96544	0.96684	0.07136	0.06827	0.66969	0.66914	0.44957	0.45604	151	151	B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	unknown	bulk	bulk	bulk	Germany	2023-08-01	Undetermined	Embryo	Whole Organism	All anatomical structures
24653	24653	SRR25487069	SRX21218618	SRS18475797	SRP452670	PRJNA1000968	CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo	GSE239788	Transcriptome Analysis	Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.		pubmed:38114601	nexn / biological replicate 1	GSM7673293	source name:whole organism\|tissue:whole organism\|genotype:nexn knockout\|geo loc name:missing\|collection date:missing	nexn / biological replicate 1	Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value	whole organism		RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics		tissue:whole organism\|genotype:nexn knockout	GSM7673293	GSM7673293: nexn / biological replicate 1; Danio rerio; RNA Seq	GSM7673293 r1	GSM7673293	1	RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP452670	loader:fastq load.py	NG-33220_nexn_E2_mut1_lib691942_10222_3_2.fastq.gz NG-33220_nexn_E2_mut1_lib691942_10222_3_1.fastq.gz	fastq fastq	6518650974.0	21584937.0	GSM7673293 r1	0:151 1:151	A:1776227735;C:1486881610;G:1503672330;T:1751641678;N:227621	151	151	1776227735	1486881610	1503672330	1751641678	227621	SRX21218618	SRS18475797	SRA1684694	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	2	0.9619	0.96365	0.08223	0.07902	0.66967	0.66811	0.44763	0.45022	151	151	B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	unknown	bulk	bulk	bulk	Germany	2023-08-01	Undetermined	Embryo	Whole Organism	All anatomical structures
24654	24654	SRR25487070	SRX21218617	SRS18475796	SRP452670	PRJNA1000968	CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo	GSE239788	Transcriptome Analysis	Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.		pubmed:38114601	nexn+/+ biological replicate 2	GSM7673292	source name:whole organism\|tissue:whole organism\|genotype:WT\|geo loc name:missing\|collection date:missing	nexn+/+ biological replicate 2	Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value	whole organism		RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics		tissue:whole organism\|genotype:WT	GSM7673292	GSM7673292: nexn+/+ biological replicate 2; Danio rerio; RNA Seq	GSM7673292 r1	GSM7673292	1	RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP452670	loader:fastq load.py	NG-33220_nexn_E2_sib3_lib693760_10227_1_1.fastq.gz NG-33220_nexn_E2_sib3_lib693760_10227_1_2.fastq.gz	fastq fastq	9966559304.0	33001852.0	GSM7673292 r1	0:151 1:151	A:2799666848;C:2201108797;G:2237142072;T:2728542087;N:99500	151	151	2799666848	2201108797	2237142072	2728542087	99500	SRX21218617	SRS18475796	SRA1684694	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	2	0.95433	0.9562	0.11378	0.10948	0.68426	0.68302	0.45622	0.46107	151	151	B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	unknown	bulk	bulk	bulk	Germany	2023-08-01	Undetermined	Embryo	Whole Organism	All anatomical structures
24655	24655	SRR25487071	SRX21218616	SRS18475795	SRP452670	PRJNA1000968	CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo	GSE239788	Transcriptome Analysis	Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.		pubmed:38114601	nexn+/+ biological replicate 1	GSM7673291	source name:whole organism\|tissue:whole organism\|genotype:WT\|geo loc name:missing\|collection date:missing	nexn+/+ biological replicate 1	Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value	whole organism		RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics		tissue:whole organism\|genotype:WT	GSM7673291	GSM7673291: nexn+/+ biological replicate 1; Danio rerio; RNA Seq	GSM7673291 r1	GSM7673291	1	RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP452670	loader:fastq load.py	NG-33220_nexn_E2_sib2_lib693759_10227_2_1.fastq.gz NG-33220_nexn_E2_sib2_lib693759_10227_2_2.fastq.gz	fastq fastq	13610380470.0	45067485.0	GSM7673291 r1	0:151 1:151	A:3776423931;C:3037607848;G:3100752195;T:3694688167;N:908329	151	151	3776423931	3037607848	3100752195	3694688167	908329	SRX21218616	SRS18475795	SRA1684694	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	Molecular Cardiology, Internal Medicine II, Uniklinik Ulm	2	0.95714	0.95793	0.10127	0.09788	0.69445	0.69278	0.47084	0.46602	151	151	B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	unknown	bulk	bulk	bulk	Germany	2023-08-01	Undetermined	Embryo	Whole Organism	All anatomical structures
25273	25273	SRR25764091	SRX21486763	SRS18719063	SRP457108	PRJNA1009807	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]	GSE241752	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326	WT bud 10 hpf RNA seq rep2	GSM7734768	source name:Gastrula\|strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT bud 10 hpf RNA seq rep2	3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation	Gastrula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|genotype:WT	GSM7734768	GSM7734768: WT bud 10 hpf RNA seq rep2; Danio rerio; RNA Seq	GSM7734768 r1	GSM7734768	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP457108		WT_mRNA_bud_2.fastq.gz	fastq	2470912004.0	31168086.0	GSM7734768 r1	0:79.28	A:656817108;C:568241258;G:504262095;T:741507737;N:83806	79		656817108	568241258	504262095	741507737	83806	SRX21486763	SRS18719063	SRA1700431	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.91479		0.27298		0.74231		0.57302		79		B		usable mapping rate	illumina	nextseq	unknown	small_rna	unknown	bulk	bulk	bulk	Germany	2023-08-28	Gastrula	Embryo	Whole Organism	All anatomical structures
25274	25274	SRR25764092	SRX21486762	SRS18719064	SRP457108	PRJNA1009807	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]	GSE241752	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326	WT bud 10 hpf RNA seq rep1	GSM7734767	source name:Gastrula\|strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT bud 10 hpf RNA seq rep1	3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation	Gastrula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|genotype:WT	GSM7734767	GSM7734767: WT bud 10 hpf RNA seq rep1; Danio rerio; RNA Seq	GSM7734767 r1	GSM7734767	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP457108		WT_mRNA_bud_1.fastq.gz	fastq	2153494756.0	27140032.0	GSM7734767 r1	0:79.35	A:560793143;C:508962676;G:445126772;T:638539310;N:72855	79		560793143	508962676	445126772	638539310	72855	SRX21486762	SRS18719064	SRA1700431	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.88728		0.25493		0.74369		0.56589		80		B		usable mapping rate	illumina	nextseq	unknown	small_rna	unknown	bulk	bulk	bulk	Germany	2023-08-28	Gastrula	Embryo	Whole Organism	All anatomical structures
25275	25275	SRR25764093	SRX21486761	SRS18719061	SRP457108	PRJNA1009807	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]	GSE241752	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326	WT sphere 4 hpf RNA seq rep2	GSM7734766	source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT sphere 4 hpf RNA seq rep2	3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|genotype:WT	GSM7734766	GSM7734766: WT sphere 4 hpf RNA seq rep2; Danio rerio; RNA Seq	GSM7734766 r1	GSM7734766	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP457108		WT_mRNA_sphere_2.fastq.gz	fastq	2455317157.0	30934591.0	GSM7734766 r1	0:79.37	A:614860604;C:588586084;G:522132289;T:729655621;N:82559	79		614860604	588586084	522132289	729655621	82559	SRX21486761	SRS18719061	SRA1700431	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.94124		0.10502		0.74876		0.57752		80		B		usable mapping rate	illumina	nextseq	unknown	small_rna	unknown	bulk	bulk	bulk	Germany	2023-08-28	Blastula	Embryo	Whole Organism	All anatomical structures
25276	25276	SRR25764094	SRX21486760	SRS18719060	SRP457108	PRJNA1009807	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]	GSE241752	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326	WT sphere 4 hpf RNA seq rep1	GSM7734765	source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT sphere 4 hpf RNA seq rep1	3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|genotype:WT	GSM7734765	GSM7734765: WT sphere 4 hpf RNA seq rep1; Danio rerio; RNA Seq	GSM7734765 r1	GSM7734765	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP457108		WT_mRNA_sphere_1.fastq.gz	fastq	2399640874.0	30232118.0	GSM7734765 r1	0:79.37	A:589069860;C:593745131;G:511439690;T:705305674;N:80519	79		589069860	593745131	511439690	705305674	80519	SRX21486760	SRS18719060	SRA1700431	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.85882		0.11848		0.75122		0.5883		80		B		usable mapping rate	illumina	nextseq	unknown	small_rna	unknown	bulk	bulk	bulk	Germany	2023-08-28	Blastula	Embryo	Whole Organism	All anatomical structures
28113	28113	SRR26209648	SRX21920662	SRS19005181	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 th…		pubmed:39437839	unDMSO t1 WT 3	GSM7812991	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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:WT\|treatment:unDMSO	GSM7812991	GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq	GSM7812991 r1	GSM7812991	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	JON686A30_S48_L005_R1_001.fastq.gz	fastq	616449359.0	6103459.0	GSM7812991 r1	0:101	A:152808626;C:149738763;G:141639387;T:172257280;N:5303	101		152808626	149738763	141639387	172257280	5303	SRX21920662	SRS19005181	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94246		0.08766		0.69443		0.4842		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
28114	28114	SRR26209649	SRX21920662	SRS19005181	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 th…		pubmed:39437839	unDMSO t1 WT 3	GSM7812991	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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:WT\|treatment:unDMSO	GSM7812991	GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq	GSM7812991 r1	GSM7812991	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	JON686A30_S48_L006_R1_001.fastq.gz	fastq	609999297.0	6039597.0	GSM7812991 r2	0:101	A:151226657;C:148143193;G:140088806;T:170530812;N:9829	101		151226657	148143193	140088806	170530812	9829	SRX21920662	SRS19005181	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94201		0.08569		0.69572		0.48692		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
28115	28115	SRR26209650	SRX21920662	SRS19005181	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 th…		pubmed:39437839	unDMSO t1 WT 3	GSM7812991	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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:WT\|treatment:unDMSO	GSM7812991	GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq	GSM7812991 r1	GSM7812991	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	JON686A30_S48_L007_R1_001.fastq.gz	fastq	543730470.0	5383470.0	GSM7812991 r3	0:101	A:134685766;C:132190291;G:124881864;T:151967639;N:4910	101		134685766	132190291	124881864	151967639	4910	SRX21920662	SRS19005181	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9431		0.08733		0.69524		0.48528		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
28116	28116	SRR26209651	SRX21920662	SRS19005181	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 th…		pubmed:39437839	unDMSO t1 WT 3	GSM7812991	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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:WT\|treatment:unDMSO	GSM7812991	GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq	GSM7812991 r1	GSM7812991	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	JON686A30_S16_L007_R1_001.fastq.gz	fastq	649354149.0	6429249.0	GSM7812991 r4	0:101	A:160756303;C:158145998;G:149623680;T:180816390;N:11778	101		160756303	158145998	149623680	180816390	11778	SRX21920662	SRS19005181	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94438		0.08618		0.69473		0.48809		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
28117	28117	SRR26209752	SRX21920662	SRS19005181	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 th…		pubmed:39437839	unDMSO t1 WT 3	GSM7812991	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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:WT\|treatment:unDMSO	GSM7812991	GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq	GSM7812991 r1	GSM7812991	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	JON686A30_S16_L008_R1_001.fastq.gz	fastq	650450504.0	6440104.0	GSM7812991 r5	0:101	A:161054597;C:158340761;G:149784923;T:181251361;N:18862	101		161054597	158340761	149784923	181251361	18862	SRX21920662	SRS19005181	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94338		0.08713		0.6968		0.48443		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
28118	28118	SRR26209652	SRX21920661	SRS19005180	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 th…		pubmed:39437839	unDMSO t1 WT 2	GSM7812990	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO	GSM7812990	GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq	GSM7812990 r1	GSM7812990	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	JON686A29_S46_L005_R1_001.fastq.gz	fastq	593068162.0	5871962.0	GSM7812990 r1	0:101	A:147906639;C:143944406;G:137307101;T:163904929;N:5087	101		147906639	143944406	137307101	163904929	5087	SRX21920661	SRS19005180	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94371		0.06473		0.69378		0.47765		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
28119	28119	SRR26209653	SRX21920661	SRS19005180	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 th…		pubmed:39437839	unDMSO t1 WT 2	GSM7812990	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO	GSM7812990	GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq	GSM7812990 r1	GSM7812990	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	JON686A29_S46_L006_R1_001.fastq.gz	fastq	588323081.0	5824981.0	GSM7812990 r2	0:101	A:146630863;C:142829925;G:136124185;T:162728186;N:9922	101		146630863	142829925	136124185	162728186	9922	SRX21920661	SRS19005180	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94282		0.06357		0.69418		0.47665		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
28120	28120	SRR26209654	SRX21920661	SRS19005180	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 th…		pubmed:39437839	unDMSO t1 WT 2	GSM7812990	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO	GSM7812990	GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq	GSM7812990 r1	GSM7812990	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	JON686A29_S46_L007_R1_001.fastq.gz	fastq	521265747.0	5161047.0	GSM7812990 r3	0:101	A:129905878;C:126622019;G:120526207;T:144206853;N:4790	101		129905878	126622019	120526207	144206853	4790	SRX21920661	SRS19005180	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94508		0.06499		0.69367		0.4834		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
28121	28121	SRR26209655	SRX21920661	SRS19005180	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 th…		pubmed:39437839	unDMSO t1 WT 2	GSM7812990	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO	GSM7812990	GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq	GSM7812990 r1	GSM7812990	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	JON686A29_S26_L007_R1_001.fastq.gz	fastq	623834580.0	6176580.0	GSM7812990 r4	0:101	A:155642981;C:151651242;G:144681951;T:171847192;N:11214	101		155642981	151651242	144681951	171847192	11214	SRX21920661	SRS19005180	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94531		0.06514		0.69225		0.48187		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
28122	28122	SRR26209656	SRX21920661	SRS19005180	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 th…		pubmed:39437839	unDMSO t1 WT 2	GSM7812990	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO	GSM7812990	GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq	GSM7812990 r1	GSM7812990	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	JON686A29_S26_L008_R1_001.fastq.gz	fastq	622155960.0	6159960.0	GSM7812990 r5	0:101	A:155145221;C:151231599;G:144290581;T:171470641;N:17918	101		155145221	151231599	144290581	171470641	17918	SRX21920661	SRS19005180	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94319		0.06413		0.69449		0.48159		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
28123	28123	SRR26209657	SRX21920660	SRS19005179	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 th…		pubmed:39437839	unDMSO t1 WT 1	GSM7812989	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 1	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:WT\|treatment:unDMSO	GSM7812989	GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq	GSM7812989 r1	GSM7812989	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	JON686A28_S45_L005_R1_001.fastq.gz	fastq	602520550.0	5965550.0	GSM7812989 r1	0:101	A:149619230;C:146559346;G:139674646;T:166662143;N:5185	101		149619230	146559346	139674646	166662143	5185	SRX21920660	SRS19005179	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94449		0.06296		0.69487		0.48		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
28124	28124	SRR26209658	SRX21920660	SRS19005179	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 th…		pubmed:39437839	unDMSO t1 WT 1	GSM7812989	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 1	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:WT\|treatment:unDMSO	GSM7812989	GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq	GSM7812989 r1	GSM7812989	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	JON686A28_S45_L006_R1_001.fastq.gz	fastq	596942522.0	5910322.0	GSM7812989 r2	0:101	A:148193962;C:145221539;G:138267073;T:165249833;N:10115	101		148193962	145221539	138267073	165249833	10115	SRX21920660	SRS19005179	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9446		0.06327		0.69562		0.48183		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
28125	28125	SRR26209659	SRX21920660	SRS19005179	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 th…		pubmed:39437839	unDMSO t1 WT 1	GSM7812989	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 1	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:WT\|treatment:unDMSO	GSM7812989	GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq	GSM7812989 r1	GSM7812989	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	JON686A28_S45_L007_R1_001.fastq.gz	fastq	532539064.0	5272664.0	GSM7812989 r3	0:101	A:132217323;C:129660296;G:123303893;T:147352732;N:4820	101		132217323	129660296	123303893	147352732	4820	SRX21920660	SRS19005179	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94579		0.06237		0.69554		0.46658		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
28126	28126	SRR26209660	SRX21920660	SRS19005179	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 th…		pubmed:39437839	unDMSO t1 WT 1	GSM7812989	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 1	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:WT\|treatment:unDMSO	GSM7812989	GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq	GSM7812989 r1	GSM7812989	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	JON686A28_S29_L007_R1_001.fastq.gz	fastq	633337569.0	6270669.0	GSM7812989 r4	0:101	A:157286526;C:154336036;G:147137950;T:174565295;N:11762	101		157286526	154336036	147137950	174565295	11762	SRX21920660	SRS19005179	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94562		0.06294		0.69489		0.47406		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
28127	28127	SRR26209661	SRX21920660	SRS19005179	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 th…		pubmed:39437839	unDMSO t1 WT 1	GSM7812989	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 WT 1	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:WT\|treatment:unDMSO	GSM7812989	GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq	GSM7812989 r1	GSM7812989	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	JON686A28_S29_L008_R1_001.fastq.gz	fastq	636051540.0	6297540.0	GSM7812989 r5	0:101	A:157845668;C:154972063;G:147765532;T:175449801;N:18476	101		157845668	154972063	147765532	175449801	18476	SRX21920660	SRS19005179	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9471		0.06288		0.69536		0.4797		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
28128	28128	SRR26209662	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 th…		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_L005_R1_001.fastq.gz	fastq	674188635.0	6675135.0	GSM7812988 r1	0:101	A:173104307;C:161481671;G:152542615;T:187053812;N:6230	101		173104307	161481671	152542615	187053812	6230	SRX21920659	SRS19005178	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94039		0.07795		0.69877		0.48386		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
28129	28129	SRR26209663	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 th…		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_L006_R1_001.fastq.gz	fastq	667048339.0	6604439.0	GSM7812988 r2	0:101	A:171316049;C:159786547;G:150743446;T:185190228;N:12069	101		171316049	159786547	150743446	185190228	12069	SRX21920659	SRS19005178	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94064		0.07881		0.69767		0.48162		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
28130	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 th…		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
28131	28131	SRR26209665	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 th…		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_S12_L007_R1_001.fastq.gz	fastq	712385926.0	7053326.0	GSM7812988 r4	0:101	A:183100436;C:171026605;G:161510527;T:196734608;N:13750	101		183100436	171026605	161510527	196734608	13750	SRX21920659	SRS19005178	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94298		0.07892		0.6997		0.48331		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
28132	28132	SRR26209666	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 th…		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_S12_L008_R1_001.fastq.gz	fastq	714661355.0	7075855.0	GSM7812988 r5	0:101	A:183454698;C:171554090;G:162064705;T:197567065;N:20797	101		183454698	171554090	162064705	197567065	20797	SRX21920659	SRS19005178	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94316		0.07877		0.70051		0.48354		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
28133	28133	SRR26209667	SRX21920658	SRS19005177	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 th…		pubmed:39437839	unDMSO t1 K2 2	GSM7812987	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO	GSM7812987	GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq	GSM7812987 r1	GSM7812987	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	JON686A35_S53_L005_R1_001.fastq.gz	fastq	611900723.0	6058423.0	GSM7812987 r1	0:101	A:154668392;C:147817141;G:139653400;T:169756342;N:5448	101		154668392	147817141	139653400	169756342	5448	SRX21920658	SRS19005177	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94636		0.08022		0.69962		0.48201		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
28134	28134	SRR26209668	SRX21920658	SRS19005177	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 th…		pubmed:39437839	unDMSO t1 K2 2	GSM7812987	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO	GSM7812987	GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq	GSM7812987 r1	GSM7812987	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	JON686A35_S53_L006_R1_001.fastq.gz	fastq	602971818.0	5970018.0	GSM7812987 r2	0:101	A:152346877;C:145640105;G:137576284;T:167398281;N:10271	101		152346877	145640105	137576284	167398281	10271	SRX21920658	SRS19005177	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94549		0.08086		0.69781		0.47842		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
28135	28135	SRR26209669	SRX21920658	SRS19005177	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 th…		pubmed:39437839	unDMSO t1 K2 2	GSM7812987	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO	GSM7812987	GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq	GSM7812987 r1	GSM7812987	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	JON686A35_S53_L007_R1_001.fastq.gz	fastq	539246575.0	5339075.0	GSM7812987 r3	0:101	A:136317506;C:130390122;G:122927887;T:149606028;N:5032	101		136317506	130390122	122927887	149606028	5032	SRX21920658	SRS19005177	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94653		0.08075		0.69704		0.48374		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
28136	28136	SRR26209670	SRX21920658	SRS19005177	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 th…		pubmed:39437839	unDMSO t1 K2 2	GSM7812987	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO	GSM7812987	GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq	GSM7812987 r1	GSM7812987	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	JON686A35_S47_L007_R1_001.fastq.gz	fastq	643197593.0	6368293.0	GSM7812987 r4	0:101	A:162743675;C:155711536;G:147135700;T:177594459;N:12223	101		162743675	155711536	147135700	177594459	12223	SRX21920658	SRS19005177	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94757		0.08023		0.70055		0.48458		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
28137	28137	SRR26209671	SRX21920658	SRS19005177	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 th…		pubmed:39437839	unDMSO t1 K2 2	GSM7812987	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO	GSM7812987	GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq	GSM7812987 r1	GSM7812987	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	JON686A35_S47_L008_R1_001.fastq.gz	fastq	644356063.0	6379763.0	GSM7812987 r5	0:101	A:162915651;C:155935181;G:147406641;T:178079118;N:19472	101		162915651	155935181	147406641	178079118	19472	SRX21920658	SRS19005177	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94817		0.08218		0.70017		0.48286		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
28138	28138	SRR26209672	SRX21920657	SRS19005176	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 th…		pubmed:39437839	unDMSO t1 K2 1	GSM7812986	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K2 1	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	GSM7812986	GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq	GSM7812986 r1	GSM7812986	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	JON686A34_S52_L005_R1_001.fastq.gz	fastq	615996374.0	6098974.0	GSM7812986 r1	0:101	A:156934542;C:147417998;G:139301915;T:172336421;N:5498	101		156934542	147417998	139301915	172336421	5498	SRX21920657	SRS19005176	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94179		0.07628		0.69512		0.48041		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
28139	28139	SRR26209673	SRX21920657	SRS19005176	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 th…		pubmed:39437839	unDMSO t1 K2 1	GSM7812986	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K2 1	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	GSM7812986	GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq	GSM7812986 r1	GSM7812986	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	JON686A34_S52_L006_R1_001.fastq.gz	fastq	608875571.0	6028471.0	GSM7812986 r2	0:101	A:155127967;C:145701864;G:137575885;T:170459017;N:10838	101		155127967	145701864	137575885	170459017	10838	SRX21920657	SRS19005176	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94248		0.07563		0.69512		0.47982		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
28140	28140	SRR26209674	SRX21920657	SRS19005176	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 th…		pubmed:39437839	unDMSO t1 K2 1	GSM7812986	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K2 1	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	GSM7812986	GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq	GSM7812986 r1	GSM7812986	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	JON686A34_S52_L007_R1_001.fastq.gz	fastq	539739455.0	5343955.0	GSM7812986 r3	0:101	A:137431217;C:129328124;G:121891472;T:151083373;N:5269	101		137431217	129328124	121891472	151083373	5269	SRX21920657	SRS19005176	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9438		0.07511		0.69654		0.48083		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
28141	28141	SRR26209675	SRX21920657	SRS19005176	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 th…		pubmed:39437839	unDMSO t1 K2 1	GSM7812986	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K2 1	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	GSM7812986	GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq	GSM7812986 r1	GSM7812986	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	JON686A34_S65_L007_R1_001.fastq.gz	fastq	648984489.0	6425589.0	GSM7812986 r4	0:101	A:165552674;C:155580501;G:147078092;T:180761105;N:12117	101		165552674	155580501	147078092	180761105	12117	SRX21920657	SRS19005176	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94513		0.07694		0.69451		0.48174		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
28142	28142	SRR26209676	SRX21920657	SRS19005176	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 th…		pubmed:39437839	unDMSO t1 K2 1	GSM7812986	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K2 1	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	GSM7812986	GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq	GSM7812986 r1	GSM7812986	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	JON686A34_S65_L008_R1_001.fastq.gz	fastq	651988330.0	6455330.0	GSM7812986 r5	0:101	A:166130853;C:156282200;G:147738788;T:181817695;N:18794	101		166130853	156282200	147738788	181817695	18794	SRX21920657	SRS19005176	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94437		0.0759		0.69597		0.48083		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
28143	28143	SRR26209677	SRX21920656	SRS19005175	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 th…		pubmed:39437839	unDMSO t1 K1 3	GSM7812985	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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:K1\|treatment:unDMSO	GSM7812985	GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq	GSM7812985 r1	GSM7812985	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	JON686A33_S51_L005_R1_001.fastq.gz	fastq	621669544.0	6155144.0	GSM7812985 r1	0:101	A:157346917;C:148083763;G:141122336;T:175110946;N:5582	101		157346917	148083763	141122336	175110946	5582	SRX21920656	SRS19005175	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94207		0.06859		0.69473		0.48838		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
28144	28144	SRR26209678	SRX21920656	SRS19005175	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 th…		pubmed:39437839	unDMSO t1 K1 3	GSM7812985	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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:K1\|treatment:unDMSO	GSM7812985	GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq	GSM7812985 r1	GSM7812985	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	JON686A33_S51_L006_R1_001.fastq.gz	fastq	613437842.0	6073642.0	GSM7812985 r2	0:101	A:155200714;C:146135271;G:139223090;T:172868018;N:10749	101		155200714	146135271	139223090	172868018	10749	SRX21920656	SRS19005175	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94144		0.06885		0.69471		0.48996		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
28145	28145	SRR26209679	SRX21920656	SRS19005175	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 th…		pubmed:39437839	unDMSO t1 K1 3	GSM7812985	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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:K1\|treatment:unDMSO	GSM7812985	GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq	GSM7812985 r1	GSM7812985	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	JON686A33_S51_L007_R1_001.fastq.gz	fastq	546684518.0	5412718.0	GSM7812985 r3	0:101	A:138292090;C:130364936;G:123978492;T:154043685;N:5315	101		138292090	130364936	123978492	154043685	5315	SRX21920656	SRS19005175	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94375		0.06988		0.69589		0.48741		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
28146	28146	SRR26209680	SRX21920656	SRS19005175	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 th…		pubmed:39437839	unDMSO t1 K1 3	GSM7812985	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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:K1\|treatment:unDMSO	GSM7812985	GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq	GSM7812985 r1	GSM7812985	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	JON686A33_S43_L007_R1_001.fastq.gz	fastq	651065089.0	6446189.0	GSM7812985 r4	0:101	A:164874330;C:155389435;G:148130531;T:182658473;N:12320	101		164874330	155389435	148130531	182658473	12320	SRX21920656	SRS19005175	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94247		0.06954		0.69538		0.48283		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
28147	28147	SRR26209681	SRX21920656	SRS19005175	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 th…		pubmed:39437839	unDMSO t1 K1 3	GSM7812985	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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:K1\|treatment:unDMSO	GSM7812985	GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq	GSM7812985 r1	GSM7812985	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	JON686A33_S43_L008_R1_001.fastq.gz	fastq	652838952.0	6463752.0	GSM7812985 r5	0:101	A:165235507;C:155756581;G:148483290;T:183344035;N:19539	101		165235507	155756581	148483290	183344035	19539	SRX21920656	SRS19005175	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94297		0.06917		0.69593		0.4827		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
28148	28148	SRR26209682	SRX21920655	SRS19005174	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 th…		pubmed:39437839	unDMSO t1 K1 2	GSM7812984	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO	GSM7812984	GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq	GSM7812984 r1	GSM7812984	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	JON686A32_S50_L005_R1_001.fastq.gz	fastq	531938215.0	5266715.0	GSM7812984 r1	0:101	A:131083905;C:128715617;G:122601298;T:149532970;N:4425	101		131083905	128715617	122601298	149532970	4425	SRX21920655	SRS19005174	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94249		0.07108		0.69485		0.47386		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
28149	28149	SRR26209683	SRX21920655	SRS19005174	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 th…		pubmed:39437839	unDMSO t1 K1 2	GSM7812984	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO	GSM7812984	GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq	GSM7812984 r1	GSM7812984	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	JON686A32_S50_L006_R1_001.fastq.gz	fastq	527781863.0	5225563.0	GSM7812984 r2	0:101	A:130119726;C:127646784;G:121549831;T:148456993;N:8529	101		130119726	127646784	121549831	148456993	8529	SRX21920655	SRS19005174	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94199		0.0713		0.69337		0.473		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
28150	28150	SRR26209684	SRX21920655	SRS19005174	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 th…		pubmed:39437839	unDMSO t1 K1 2	GSM7812984	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO	GSM7812984	GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq	GSM7812984 r1	GSM7812984	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	JON686A32_S50_L007_R1_001.fastq.gz	fastq	472785040.0	4681040.0	GSM7812984 r3	0:101	A:116503463;C:114489771;G:108989839;T:132797698;N:4269	101		116503463	114489771	108989839	132797698	4269	SRX21920655	SRS19005174	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94373		0.07285		0.69467		0.47913		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
28151	28151	SRR26209685	SRX21920655	SRS19005174	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 th…		pubmed:39437839	unDMSO t1 K1 2	GSM7812984	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO	GSM7812984	GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq	GSM7812984 r1	GSM7812984	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	JON686A32_S71_L007_R1_001.fastq.gz	fastq	561056414.0	5555014.0	GSM7812984 r4	0:101	A:138240115;C:136040813;G:129592563;T:157172399;N:10524	101		138240115	136040813	129592563	157172399	10524	SRX21920655	SRS19005174	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94357		0.07109		0.69544		0.47169		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
28152	28152	SRR26209686	SRX21920655	SRS19005174	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 th…		pubmed:39437839	unDMSO t1 K1 2	GSM7812984	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO	GSM7812984	GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq	GSM7812984 r1	GSM7812984	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	JON686A32_S71_L008_R1_001.fastq.gz	fastq	563109744.0	5575344.0	GSM7812984 r5	0:101	A:138778764;C:136444809;G:129964766;T:157904708;N:16697	101		138778764	136444809	129964766	157904708	16697	SRX21920655	SRS19005174	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94358		0.07253		0.69345		0.47443		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
28153	28153	SRR26209687	SRX21920654	SRS19005173	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 th…		pubmed:39437839	unDMSO t1 K1 1	GSM7812983	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 1	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:K1\|treatment:unDMSO	GSM7812983	GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq	GSM7812983 r1	GSM7812983	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	JON686A31_S49_L005_R1_001.fastq.gz	fastq	576725857.0	5710157.0	GSM7812983 r1	0:101	A:142557020;C:140092748;G:133378036;T:160693137;N:4916	101		142557020	140092748	133378036	160693137	4916	SRX21920654	SRS19005173	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94239		0.07259		0.69398		0.47675		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
28154	28154	SRR26209688	SRX21920654	SRS19005173	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 th…		pubmed:39437839	unDMSO t1 K1 1	GSM7812983	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 1	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:K1\|treatment:unDMSO	GSM7812983	GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq	GSM7812983 r1	GSM7812983	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	JON686A31_S49_L006_R1_001.fastq.gz	fastq	569166310.0	5635310.0	GSM7812983 r2	0:101	A:140702145;C:138232540;G:131558917;T:158663414;N:9294	101		140702145	138232540	131558917	158663414	9294	SRX21920654	SRS19005173	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94221		0.07252		0.69524		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
28155	28155	SRR26209689	SRX21920654	SRS19005173	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 th…		pubmed:39437839	unDMSO t1 K1 1	GSM7812983	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 1	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:K1\|treatment:unDMSO	GSM7812983	GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq	GSM7812983 r1	GSM7812983	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	JON686A31_S49_L007_R1_001.fastq.gz	fastq	505699425.0	5006925.0	GSM7812983 r3	0:101	A:124940125;C:122891114;G:116919354;T:140944307;N:4525	101		124940125	122891114	116919354	140944307	4525	SRX21920654	SRS19005173	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.944		0.07242		0.69473		0.48289		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
28156	28156	SRR26209690	SRX21920654	SRS19005173	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 th…		pubmed:39437839	unDMSO t1 K1 1	GSM7812983	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 1	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:K1\|treatment:unDMSO	GSM7812983	GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq	GSM7812983 r1	GSM7812983	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	JON686A31_S27_L007_R1_001.fastq.gz	fastq	598624374.0	5926974.0	GSM7812983 r4	0:101	A:147863525;C:145723385;G:138724140;T:166302217;N:11107	101		147863525	145723385	138724140	166302217	11107	SRX21920654	SRS19005173	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94426		0.07312		0.69479		0.48056		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
28157	28157	SRR26209691	SRX21920654	SRS19005173	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 th…		pubmed:39437839	unDMSO t1 K1 1	GSM7812983	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:unDMSO\|geo loc name:missing\|collection date:missing	unDMSO t1 K1 1	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:K1\|treatment:unDMSO	GSM7812983	GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq	GSM7812983 r1	GSM7812983	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	JON686A31_S27_L008_R1_001.fastq.gz	fastq	602654072.0	5966872.0	GSM7812983 r5	0:101	A:148869054;C:146693906;G:139571739;T:167501958;N:17415	101		148869054	146693906	139571739	167501958	17415	SRX21920654	SRS19005173	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9433		0.0732		0.69552		0.47807		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
28158	28158	SRR26209692	SRX21920653	SRS19005172	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 th…		pubmed:39437839	IR t2 WT 3	GSM7812982	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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:t2\|genotype:WT\|treatment:IR	GSM7812982	GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq	GSM7812982 r1	GSM7812982	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	JON686A21_S38_L005_R1_001.fastq.gz	fastq	617990619.0	6118719.0	GSM7812982 r1	0:101	A:155764078;C:148642484;G:140551460;T:173027146;N:5451	101		155764078	148642484	140551460	173027146	5451	SRX21920653	SRS19005172	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93982		0.07316		0.68801		0.48964		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
28159	28159	SRR26209693	SRX21920653	SRS19005172	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 th…		pubmed:39437839	IR t2 WT 3	GSM7812982	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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:t2\|genotype:WT\|treatment:IR	GSM7812982	GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq	GSM7812982 r1	GSM7812982	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	JON686A21_S38_L006_R1_001.fastq.gz	fastq	612677312.0	6066112.0	GSM7812982 r2	0:101	A:154425053;C:147379484;G:139208932;T:171653577;N:10266	101		154425053	147379484	139208932	171653577	10266	SRX21920653	SRS19005172	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93954		0.07439		0.68945		0.48768		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
28160	28160	SRR26209694	SRX21920653	SRS19005172	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 th…		pubmed:39437839	IR t2 WT 3	GSM7812982	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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:t2\|genotype:WT\|treatment:IR	GSM7812982	GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq	GSM7812982 r1	GSM7812982	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	JON686A21_S38_L007_R1_001.fastq.gz	fastq	545311221.0	5399121.0	GSM7812982 r3	0:101	A:137422024;C:131281461;G:123803444;T:152799164;N:5128	101		137422024	131281461	123803444	152799164	5128	SRX21920653	SRS19005172	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94119		0.07433		0.6886		0.48763		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
28161	28161	SRR26209695	SRX21920653	SRS19005172	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 th…		pubmed:39437839	IR t2 WT 3	GSM7812982	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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:t2\|genotype:WT\|treatment:IR	GSM7812982	GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq	GSM7812982 r1	GSM7812982	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	JON686A21_S68_L007_R1_001.fastq.gz	fastq	643233246.0	6368646.0	GSM7812982 r4	0:101	A:162062613;C:155064589;G:146625670;T:179468362;N:12012	101		162062613	155064589	146625670	179468362	12012	SRX21920653	SRS19005172	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94076		0.07335		0.68747		0.48953		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
28162	28162	SRR26209696	SRX21920653	SRS19005172	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 th…		pubmed:39437839	IR t2 WT 3	GSM7812982	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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:t2\|genotype:WT\|treatment:IR	GSM7812982	GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq	GSM7812982 r1	GSM7812982	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	JON686A21_S68_L008_R1_001.fastq.gz	fastq	643010339.0	6366439.0	GSM7812982 r5	0:101	A:161939065;C:154897858;G:146526716;T:179627762;N:18938	101		161939065	154897858	146526716	179627762	18938	SRX21920653	SRS19005172	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94077		0.07428		0.68852		0.4878		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
28163	28163	SRR26209697	SRX21920652	SRS19005171	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 th…		pubmed:39437839	IR t2 WT 2	GSM7812981	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR	GSM7812981	GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq	GSM7812981 r1	GSM7812981	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	JON686A20_S37_L005_R1_001.fastq.gz	fastq	608303002.0	6022802.0	GSM7812981 r1	0:101	A:151266125;C:146608795;G:139308397;T:171114479;N:5206	101		151266125	146608795	139308397	171114479	5206	SRX21920652	SRS19005171	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9409		0.06934		0.68702		0.48691		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
28164	28164	SRR26209698	SRX21920652	SRS19005171	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 th…		pubmed:39437839	IR t2 WT 2	GSM7812981	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR	GSM7812981	GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq	GSM7812981 r1	GSM7812981	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	JON686A20_S37_L006_R1_001.fastq.gz	fastq	602278857.0	5963157.0	GSM7812981 r2	0:101	A:149885037;C:145060278;G:137831227;T:169492101;N:10214	101		149885037	145060278	137831227	169492101	10214	SRX21920652	SRS19005171	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94168		0.06967		0.68491		0.48684		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
28165	28165	SRR26209699	SRX21920652	SRS19005171	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 th…		pubmed:39437839	IR t2 WT 2	GSM7812981	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR	GSM7812981	GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq	GSM7812981 r1	GSM7812981	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	JON686A20_S37_L007_R1_001.fastq.gz	fastq	539699863.0	5343563.0	GSM7812981 r3	0:101	A:134101752;C:130207416;G:123553593;T:151832349;N:4753	101		134101752	130207416	123553593	151832349	4753	SRX21920652	SRS19005171	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94262		0.06995		0.68605		0.48097		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
28166	28166	SRR26209700	SRX21920652	SRS19005171	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 th…		pubmed:39437839	IR t2 WT 2	GSM7812981	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR	GSM7812981	GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq	GSM7812981 r1	GSM7812981	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	JON686A20_S13_L007_R1_001.fastq.gz	fastq	629529263.0	6232963.0	GSM7812981 r4	0:101	A:156345013;C:152106432;G:144536894;T:176529480;N:11444	101		156345013	152106432	144536894	176529480	11444	SRX21920652	SRS19005171	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94267		0.06864		0.68477		0.47912		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
28167	28167	SRR26209701	SRX21920652	SRS19005171	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 th…		pubmed:39437839	IR t2 WT 2	GSM7812981	source name:whole embryo\|tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR\|geo loc name:missing\|collection date:missing	IR t2 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t2\|genotype:WT\|treatment:IR	GSM7812981	GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq	GSM7812981 r1	GSM7812981	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	JON686A20_S13_L008_R1_001.fastq.gz	fastq	633828732.0	6275532.0	GSM7812981 r5	0:101	A:157411401;C:153033686;G:145422340;T:177942918;N:18387	101		157411401	153033686	145422340	177942918	18387	SRX21920652	SRS19005171	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94386		0.06993		0.68479		0.48216		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
28168	28168	SRR26209702	SRX21920651	SRS19005170	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 th…		pubmed:39437839	un t1 WT 3	GSM7813000	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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:WT\|treatment:un	GSM7813000	GSM7813000: un t1 WT 3; Danio rerio; RNA Seq	GSM7813000 r1	GSM7813000	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	JON686A3_S47_L005_R1_001.fastq.gz	fastq	576015423.0	5703123.0	GSM7813000 r1	0:101	A:142483427;C:134492274;G:128574929;T:170459571;N:5222	101		142483427	134492274	128574929	170459571	5222	SRX21920651	SRS19005170	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93576		0.07681		0.6939		0.4794		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
28169	28169	SRR26209703	SRX21920651	SRS19005170	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 th…		pubmed:39437839	un t1 WT 3	GSM7813000	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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:WT\|treatment:un	GSM7813000	GSM7813000: un t1 WT 3; Danio rerio; RNA Seq	GSM7813000 r1	GSM7813000	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	JON686A3_S47_L006_R1_001.fastq.gz	fastq	568813012.0	5631812.0	GSM7813000 r2	0:101	A:140699035;C:132793802;G:126863421;T:168447319;N:9435	101		140699035	132793802	126863421	168447319	9435	SRX21920651	SRS19005170	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93455		0.07506		0.69229		0.47926		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
28170	28170	SRR26209704	SRX21920651	SRS19005170	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 th…		pubmed:39437839	un t1 WT 3	GSM7813000	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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:WT\|treatment:un	GSM7813000	GSM7813000: un t1 WT 3; Danio rerio; RNA Seq	GSM7813000 r1	GSM7813000	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	JON686A3_S47_L007_R1_001.fastq.gz	fastq	510666908.0	5056108.0	GSM7813000 r3	0:101	A:126264547;C:119308486;G:114018656;T:151070721;N:4498	101		126264547	119308486	114018656	151070721	4498	SRX21920651	SRS19005170	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93621		0.07582		0.6928		0.48424		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
28171	28171	SRR26209705	SRX21920651	SRS19005170	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 th…		pubmed:39437839	un t1 WT 3	GSM7813000	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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:WT\|treatment:un	GSM7813000	GSM7813000: un t1 WT 3; Danio rerio; RNA Seq	GSM7813000 r1	GSM7813000	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	JON686A3_S5_L007_R1_001.fastq.gz	fastq	602866980.0	5968980.0	GSM7813000 r4	0:101	A:148987273;C:141267314;G:134805122;T:177796181;N:11090	101		148987273	141267314	134805122	177796181	11090	SRX21920651	SRS19005170	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93771		0.07611		0.69305		0.48012		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
28172	28172	SRR26209706	SRX21920651	SRS19005170	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 th…		pubmed:39437839	un t1 WT 3	GSM7813000	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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:WT\|treatment:un	GSM7813000	GSM7813000: un t1 WT 3; Danio rerio; RNA Seq	GSM7813000 r1	GSM7813000	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	JON686A3_S5_L008_R1_001.fastq.gz	fastq	605447934.0	5994534.0	GSM7813000 r5	0:101	A:149696103;C:141763945;G:135323063;T:178646888;N:17935	101		149696103	141763945	135323063	178646888	17935	SRX21920651	SRS19005170	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93786		0.0763		0.6911		0.48344		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
28173	28173	SRR26209709	SRX21920650	SRS19005168	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 th…		pubmed:39437839	un t1 WT 2	GSM7812999	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un	GSM7812999	GSM7812999: un t1 WT 2; Danio rerio; RNA Seq	GSM7812999 r1	GSM7812999	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	JON686A2_S36_L005_R1_001.fastq.gz	fastq	556466166.0	5509566.0	GSM7812999 r1	0:101	A:139611141;C:131729703;G:125284158;T:159836124;N:5040	101		139611141	131729703	125284158	159836124	5040	SRX21920650	SRS19005168	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93631		0.07619		0.69016		0.47322		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
28174	28174	SRR26209710	SRX21920650	SRS19005168	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 th…		pubmed:39437839	un t1 WT 2	GSM7812999	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un	GSM7812999	GSM7812999: un t1 WT 2; Danio rerio; RNA Seq	GSM7812999 r1	GSM7812999	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	JON686A2_S36_L006_R1_001.fastq.gz	fastq	550955707.0	5455007.0	GSM7812999 r2	0:101	A:138283185;C:130378801;G:123913867;T:158370327;N:9527	101		138283185	130378801	123913867	158370327	9527	SRX21920650	SRS19005168	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93674		0.07558		0.69018		0.47446		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
28175	28175	SRR26209711	SRX21920650	SRS19005168	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 th…		pubmed:39437839	un t1 WT 2	GSM7812999	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un	GSM7812999	GSM7812999: un t1 WT 2; Danio rerio; RNA Seq	GSM7812999 r1	GSM7812999	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	JON686A2_S36_L007_R1_001.fastq.gz	fastq	489105125.0	4842625.0	GSM7812999 r3	0:101	A:122641903;C:115831859;G:110132706;T:140494104;N:4553	101		122641903	115831859	110132706	140494104	4553	SRX21920650	SRS19005168	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93871		0.07529		0.69067		0.47657		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
28176	28176	SRR26209712	SRX21920650	SRS19005168	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 th…		pubmed:39437839	un t1 WT 2	GSM7812999	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un	GSM7812999	GSM7812999: un t1 WT 2; Danio rerio; RNA Seq	GSM7812999 r1	GSM7812999	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	JON686A2_S52_L007_R1_001.fastq.gz	fastq	584149862.0	5783662.0	GSM7812999 r4	0:101	A:146448684;C:138570019;G:131766472;T:167353726;N:10961	101		146448684	138570019	131766472	167353726	10961	SRX21920650	SRS19005168	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93862		0.07597		0.69037		0.47425		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
28177	28177	SRR26209713	SRX21920650	SRS19005168	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 th…		pubmed:39437839	un t1 WT 2	GSM7812999	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un	GSM7812999	GSM7812999: un t1 WT 2; Danio rerio; RNA Seq	GSM7812999 r1	GSM7812999	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	JON686A2_S52_L008_R1_001.fastq.gz	fastq	587223595.0	5814095.0	GSM7812999 r5	0:101	A:147280051;C:139251420;G:132358015;T:168316824;N:17285	101		147280051	139251420	132358015	168316824	17285	SRX21920650	SRS19005168	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93908		0.07566		0.69051		0.47457		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
28178	28178	SRR26209714	SRX21920649	SRS19005169	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 th…		pubmed:39437839	un t1 WT 1	GSM7812998	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 1	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:WT\|treatment:un	GSM7812998	GSM7812998: un t1 WT 1; Danio rerio; RNA Seq	GSM7812998 r1	GSM7812998	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	JON686A1_S25_L005_R1_001.fastq.gz	fastq	586786669.0	5809769.0	GSM7812998 r1	0:101	A:146663914;C:138395633;G:131925721;T:169796344;N:5057	101		146663914	138395633	131925721	169796344	5057	SRX21920649	SRS19005169	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93799		0.0785		0.68921		0.47635		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
28179	28179	SRR26209715	SRX21920649	SRS19005169	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 th…		pubmed:39437839	un t1 WT 1	GSM7812998	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 1	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:WT\|treatment:un	GSM7812998	GSM7812998: un t1 WT 1; Danio rerio; RNA Seq	GSM7812998 r1	GSM7812998	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	JON686A1_S25_L006_R1_001.fastq.gz	fastq	580037142.0	5742942.0	GSM7812998 r2	0:101	A:145023616;C:136736616;G:130314515;T:167952749;N:9646	101		145023616	136736616	130314515	167952749	9646	SRX21920649	SRS19005169	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9375		0.0778		0.69126		0.4693		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
28180	28180	SRR26209716	SRX21920649	SRS19005169	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 th…		pubmed:39437839	un t1 WT 1	GSM7812998	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 1	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:WT\|treatment:un	GSM7812998	GSM7812998: un t1 WT 1; Danio rerio; RNA Seq	GSM7812998 r1	GSM7812998	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	JON686A1_S25_L007_R1_001.fastq.gz	fastq	520166160.0	5150160.0	GSM7812998 r3	0:101	A:129930970;C:122767131;G:117052309;T:150411128;N:4622	101		129930970	122767131	117052309	150411128	4622	SRX21920649	SRS19005169	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93856		0.07769		0.68986		0.47872		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
28181	28181	SRR26209717	SRX21920649	SRS19005169	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 th…		pubmed:39437839	un t1 WT 1	GSM7812998	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 1	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:WT\|treatment:un	GSM7812998	GSM7812998: un t1 WT 1; Danio rerio; RNA Seq	GSM7812998 r1	GSM7812998	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	JON686A1_S38_L007_R1_001.fastq.gz	fastq	613687716.0	6076116.0	GSM7812998 r4	0:101	A:153144671;C:145096423;G:138249991;T:177185506;N:11125	101		153144671	145096423	138249991	177185506	11125	SRX21920649	SRS19005169	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93852		0.07714		0.69114		0.47286		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
28182	28182	SRR26209718	SRX21920649	SRS19005169	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 th…		pubmed:39437839	un t1 WT 1	GSM7812998	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:WT\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 WT 1	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:WT\|treatment:un	GSM7812998	GSM7812998: un t1 WT 1; Danio rerio; RNA Seq	GSM7812998 r1	GSM7812998	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	JON686A1_S38_L008_R1_001.fastq.gz	fastq	616318665.0	6102165.0	GSM7812998 r5	0:101	A:153949045;C:145626513;G:138751875;T:177973081;N:18151	101		153949045	145626513	138751875	177973081	18151	SRX21920649	SRS19005169	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93903		0.07786		0.68988		0.47636		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
28183	28183	SRR26209719	SRX21920648	SRS19005167	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 th…		pubmed:39437839	un t1 K2 3	GSM7812997	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un 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:un	GSM7812997	GSM7812997: un t1 K2 3; Danio rerio; RNA Seq	GSM7812997 r1	GSM7812997	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	JON686A9_S78_L005_R1_001.fastq.gz	fastq	724244336.0	7170736.0	GSM7812997 r1	0:101	A:186549355;C:171075233;G:162480404;T:204132811;N:6533	101		186549355	171075233	162480404	204132811	6533	SRX21920648	SRS19005167	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93859		0.0781		0.69398		0.47368		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
28184	28184	SRR26209720	SRX21920648	SRS19005167	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 th…		pubmed:39437839	un t1 K2 3	GSM7812997	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un 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:un	GSM7812997	GSM7812997: un t1 K2 3; Danio rerio; RNA Seq	GSM7812997 r1	GSM7812997	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	JON686A9_S78_L006_R1_001.fastq.gz	fastq	715170900.0	7080900.0	GSM7812997 r2	0:101	A:184237250;C:168924034;G:160306739;T:201690849;N:12028	101		184237250	168924034	160306739	201690849	12028	SRX21920648	SRS19005167	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9387		0.07758		0.69351		0.47477		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
28185	28185	SRR26209721	SRX21920648	SRS19005167	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 th…		pubmed:39437839	un t1 K2 3	GSM7812997	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un 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:un	GSM7812997	GSM7812997: un t1 K2 3; Danio rerio; RNA Seq	GSM7812997 r1	GSM7812997	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	JON686A9_S78_L007_R1_001.fastq.gz	fastq	640321517.0	6339817.0	GSM7812997 r3	0:101	A:164839141;C:151424251;G:143417815;T:180634187;N:6123	101		164839141	151424251	143417815	180634187	6123	SRX21920648	SRS19005167	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93922		0.07776		0.69704		0.47799		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
28186	28186	SRR26209722	SRX21920648	SRS19005167	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 th…		pubmed:39437839	un t1 K2 3	GSM7812997	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un 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:un	GSM7812997	GSM7812997: un t1 K2 3; Danio rerio; RNA Seq	GSM7812997 r1	GSM7812997	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	JON686A9_S40_L007_R1_001.fastq.gz	fastq	761823507.0	7542807.0	GSM7812997 r4	0:101	A:196286252;C:180257625;G:171369071;T:213896271;N:14288	101		196286252	180257625	171369071	213896271	14288	SRX21920648	SRS19005167	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9401		0.07711		0.69432		0.47434		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
28187	28187	SRR26209723	SRX21920648	SRS19005167	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 th…		pubmed:39437839	un t1 K2 3	GSM7812997	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un 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:un	GSM7812997	GSM7812997: un t1 K2 3; Danio rerio; RNA Seq	GSM7812997 r1	GSM7812997	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	JON686A9_S40_L008_R1_001.fastq.gz	fastq	766290434.0	7587034.0	GSM7812997 r5	0:101	A:197350392;C:181234905;G:172326999;T:215355106;N:23032	101		197350392	181234905	172326999	215355106	23032	SRX21920648	SRS19005167	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94063		0.07837		0.69286		0.47547		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
28188	28188	SRR26209724	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 th…		pubmed:39437839	un t1 K2 2	GSM7812996	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 ⋜ 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	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP463749	loader:fastq load.py	JON686A8_S77_L005_R1_001.fastq.gz	fastq	593569122.0	5876922.0	GSM7812996 r1	0:101	A:149278073;C:141195461;G:134126340;T:168963965;N:5283	101		149278073	141195461	134126340	168963965	5283	SRX21920647	SRS19005166	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93767		0.07505		0.69146		0.4769		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
28189	28189	SRR26209725	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 th…		pubmed:39437839	un t1 K2 2	GSM7812996	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 ⋜ 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	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP463749	loader:fastq load.py	JON686A8_S77_L006_R1_001.fastq.gz	fastq	589735768.0	5838968.0	GSM7812996 r2	0:101	A:148392810;C:140188863;G:133132306;T:168011761;N:10028	101		148392810	140188863	133132306	168011761	10028	SRX21920647	SRS19005166	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93804		0.07637		0.69112		0.47875		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
28190	28190	SRR26209726	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 th…		pubmed:39437839	un t1 K2 2	GSM7812996	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 ⋜ 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	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP463749	loader:fastq load.py	JON686A8_S77_L007_R1_001.fastq.gz	fastq	527272217.0	5220517.0	GSM7812996 r3	0:101	A:132562535;C:125471545;G:119166731;T:150066425;N:4981	101		132562535	125471545	119166731	150066425	4981	SRX21920647	SRS19005166	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93967		0.07529		0.69138		0.47674		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
28191	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 th…		pubmed:39437839	un t1 K2 2	GSM7812996	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 ⋜ 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	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP463749	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		157368110	149165182	141695477	177678522	11525	SRX21920647	SRS19005166	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9397		0.07494		0.69098		0.47166		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
28192	28192	SRR26209728	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 th…		pubmed:39437839	un t1 K2 2	GSM7812996	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 ⋜ 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	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP463749	loader:fastq load.py	JON686A8_S23_L008_R1_001.fastq.gz	fastq	627642987.0	6214287.0	GSM7812996 r5	0:101	A:157833602;C:149532903;G:142007778;T:178250148;N:18556	101		157833602	149532903	142007778	178250148	18556	SRX21920647	SRS19005166	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93937		0.07383		0.69264		0.46903		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
28193	28193	SRR26209729	SRX21920646	SRS19005165	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 th…		pubmed:39437839	un t1 K2 1	GSM7812995	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K2 1	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:un	GSM7812995	GSM7812995: un t1 K2 1; Danio rerio; RNA Seq	GSM7812995 r1	GSM7812995	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	JON686A7_S76_L005_R1_001.fastq.gz	fastq	557161753.0	5516453.0	GSM7812995 r1	0:101	A:139596521;C:131831457;G:125907167;T:159821690;N:4918	101		139596521	131831457	125907167	159821690	4918	SRX21920646	SRS19005165	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93861		0.07458		0.69292		0.47371		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
28194	28194	SRR26209730	SRX21920646	SRS19005165	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 th…		pubmed:39437839	un t1 K2 1	GSM7812995	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K2 1	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:un	GSM7812995	GSM7812995: un t1 K2 1; Danio rerio; RNA Seq	GSM7812995 r1	GSM7812995	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	JON686A7_S76_L006_R1_001.fastq.gz	fastq	550172856.0	5447256.0	GSM7812995 r2	0:101	A:137900064;C:130137634;G:124245600;T:157880305;N:9253	101		137900064	130137634	124245600	157880305	9253	SRX21920646	SRS19005165	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93743		0.07438		0.6927		0.46612		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
28195	28195	SRR26209731	SRX21920646	SRS19005165	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 th…		pubmed:39437839	un t1 K2 1	GSM7812995	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K2 1	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:un	GSM7812995	GSM7812995: un t1 K2 1; Danio rerio; RNA Seq	GSM7812995 r1	GSM7812995	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	JON686A7_S76_L007_R1_001.fastq.gz	fastq	491286321.0	4864221.0	GSM7812995 r3	0:101	A:123003877;C:116341215;G:111062034;T:140874602;N:4593	101		123003877	116341215	111062034	140874602	4593	SRX21920646	SRS19005165	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93869		0.07274		0.69077		0.47295		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
28196	28196	SRR26209732	SRX21920646	SRS19005165	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 th…		pubmed:39437839	un t1 K2 1	GSM7812995	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K2 1	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:un	GSM7812995	GSM7812995: un t1 K2 1; Danio rerio; RNA Seq	GSM7812995 r1	GSM7812995	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	JON686A7_S32_L007_R1_001.fastq.gz	fastq	577161975.0	5714475.0	GSM7812995 r4	0:101	A:144483271;C:136876664;G:130683956;T:165107465;N:10619	101		144483271	136876664	130683956	165107465	10619	SRX21920646	SRS19005165	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93865		0.07406		0.69203		0.46021		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
28197	28197	SRR26209733	SRX21920646	SRS19005165	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 th…		pubmed:39437839	un t1 K2 1	GSM7812995	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K2\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K2 1	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:un	GSM7812995	GSM7812995: un t1 K2 1; Danio rerio; RNA Seq	GSM7812995 r1	GSM7812995	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	JON686A7_S32_L008_R1_001.fastq.gz	fastq	582306208.0	5765408.0	GSM7812995 r5	0:101	A:145810013;C:138058537;G:131781643;T:166638883;N:17132	101		145810013	138058537	131781643	166638883	17132	SRX21920646	SRS19005165	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93981		0.07365		0.6925		0.47491		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
28198	28198	SRR26209734	SRX21920645	SRS19005164	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 th…		pubmed:39437839	un t1 K1 3	GSM7812994	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K1 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:K1\|treatment:un	GSM7812994	GSM7812994: un t1 K1 3; Danio rerio; RNA Seq	GSM7812994 r1	GSM7812994	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	JON686A6_S75_L005_R1_001.fastq.gz	fastq	585188041.0	5793941.0	GSM7812994 r1	0:101	A:146187444;C:139060409;G:132313266;T:167621845;N:5077	101		146187444	139060409	132313266	167621845	5077	SRX21920645	SRS19005164	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93793		0.07294		0.69223		0.46629		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
28199	28199	SRR26209735	SRX21920645	SRS19005164	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 th…		pubmed:39437839	un t1 K1 3	GSM7812994	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K1 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:K1\|treatment:un	GSM7812994	GSM7812994: un t1 K1 3; Danio rerio; RNA Seq	GSM7812994 r1	GSM7812994	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	JON686A6_S75_L006_R1_001.fastq.gz	fastq	580715559.0	5749659.0	GSM7812994 r2	0:101	A:145163669;C:137998922;G:131187804;T:166355185;N:9979	101		145163669	137998922	131187804	166355185	9979	SRX21920645	SRS19005164	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93853		0.0729		0.69035		0.47625		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
28200	28200	SRR26209736	SRX21920645	SRS19005164	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 th…		pubmed:39437839	un t1 K1 3	GSM7812994	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K1 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:K1\|treatment:un	GSM7812994	GSM7812994: un t1 K1 3; Danio rerio; RNA Seq	GSM7812994 r1	GSM7812994	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	JON686A6_S75_L007_R1_001.fastq.gz	fastq	517815688.0	5126888.0	GSM7812994 r3	0:101	A:129297035;C:123107269;G:117117190;T:148289396;N:4798	101		129297035	123107269	117117190	148289396	4798	SRX21920645	SRS19005164	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.9397		0.07185		0.69234		0.47459		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
28201	28201	SRR26209737	SRX21920645	SRS19005164	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 th…		pubmed:39437839	un t1 K1 3	GSM7812994	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K1 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:K1\|treatment:un	GSM7812994	GSM7812994: un t1 K1 3; Danio rerio; RNA Seq	GSM7812994 r1	GSM7812994	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	JON686A6_S50_L007_R1_001.fastq.gz	fastq	613195038.0	6071238.0	GSM7812994 r4	0:101	A:152868207;C:146093024;G:138971001;T:175251600;N:11206	101		152868207	146093024	138971001	175251600	11206	SRX21920645	SRS19005164	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93936		0.07123		0.69333		0.47591		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
28202	28202	SRR26209738	SRX21920645	SRS19005164	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 th…		pubmed:39437839	un t1 K1 3	GSM7812994	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K1 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:K1\|treatment:un	GSM7812994	GSM7812994: un t1 K1 3; Danio rerio; RNA Seq	GSM7812994 r1	GSM7812994	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	JON686A6_S50_L008_R1_001.fastq.gz	fastq	615596717.0	6095017.0	GSM7812994 r5	0:101	A:153526888;C:146591967;G:139462033;T:175997911;N:17918	101		153526888	146591967	139462033	175997911	17918	SRX21920645	SRS19005164	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93993		0.07151		0.6913		0.47319		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
28203	28203	SRR26209739	SRX21920644	SRS19005163	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 th…		pubmed:39437839	un t1 K1 2	GSM7812993	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K1 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un	GSM7812993	GSM7812993: un t1 K1 2; Danio rerio; RNA Seq	GSM7812993 r1	GSM7812993	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	JON686A5_S69_L005_R1_001.fastq.gz	fastq	577110162.0	5713962.0	GSM7812993 r1	0:101	A:143222126;C:138374184;G:131796695;T:163711998;N:5159	101		143222126	138374184	131796695	163711998	5159	SRX21920644	SRS19005163	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.94035		0.06827		0.69075		0.48076		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
28204	28204	SRR26209740	SRX21920644	SRS19005163	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 th…		pubmed:39437839	un t1 K1 2	GSM7812993	source name:whole embryo\|tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un\|geo loc name:missing\|collection date:missing	un t1 K1 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 ⋜ 50 embryos	tissue:whole embryo\|timepoint:t1\|genotype:K1\|treatment:un	GSM7812993	GSM7812993: un t1 K1 2; Danio rerio; RNA Seq	GSM7812993 r1	GSM7812993	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	JON686A5_S69_L006_R1_001.fastq.gz	fastq	573510724.0	5678324.0	GSM7812993 r2	0:101	A:142304701;C:137466974;G:130913504;T:162815434;N:10111	101		142304701	137466974	130913504	162815434	10111	SRX21920644	SRS19005163	SRA1722794	Devenport, Molecular Biology, Princeton University	Devenport, Molecular Biology, Princeton University	1	0.93982		0.06886		0.69359		0.47999		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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;