rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 10391,ERR8516975,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R,0:51 1:51,A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852,51,51,,,1077092958,949537387,955020348,1099432979,20556852,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.9053,0.9259,0.21658,0.22155,0.69369,0.69179,0.50726,0.50871,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10392,ERR8516976,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R,0:51 1:51,A:972081222;C:890179393;G:888655698;T:998443264;N:18934747,51,51,,,972081222,890179393,888655698,998443264,18934747,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.86107,0.87807,0.22063,0.23029,0.70859,0.70561,0.51656,0.51946,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10393,ERR8516977,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R,0:51 1:51,A:728798881;C:962223604;G:958876331;T:735449513;N:17094231,51,51,,,728798881,962223604,958876331,735449513,17094231,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.54616,0.55881,0.13313,0.14036,0.84295,0.84185,0.64193,0.59762,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10394,ERR8516972,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R,0:51 1:51,A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786,51,51,,,837274632,1062368015,1049892288,853310517,19213786,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.5726,0.57788,0.13781,0.14082,0.80616,0.80452,0.61581,0.60389,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10395,ERR8516973,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R,0:51 1:51,A:897813231;C:796012893;G:794839496;T:923696030;N:17221274,51,51,,,897813231,796012893,794839496,923696030,17221274,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.92095,0.94156,0.18892,0.20024,0.6901,0.68905,0.49377,0.50086,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10396,ERR8516974,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R,0:51 1:51,A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248,51,51,,,951912827,1107150666,1086060798,973791571,20785248,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.63792,0.62667,0.18547,0.18671,0.78756,0.78549,0.59274,0.55478,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10397,ERR8516969,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R,0:51 1:51,A:925784769;C:934445856;G:959155668;T:924080408;N:18878983,51,51,,,925784769,934445856,959155668,924080408,18878983,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.59503,0.61112,0.1947,0.20225,0.76512,0.76337,0.54584,0.54345,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10398,ERR8516970,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R,0:51 1:51,A:991755033;C:864808531;G:892202564;T:992188806;N:18881958,51,51,,,991755033,864808531,892202564,992188806,18881958,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.86612,0.88689,0.26181,0.2728,0.7094,0.7091,0.53639,0.53906,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10399,ERR8516971,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R,0:51 1:51,A:766707527;C:798667604;G:818782599;T:773280942;N:15938306,51,51,,,766707527,798667604,818782599,773280942,15938306,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.88811,0.92834,0.21869,0.22669,0.72878,0.72604,0.55598,0.57831,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10400,ERR8516966,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R,0:51 1:51,A:774360373;C:720215184;G:719479745;T:796239200;N:15182374,51,51,,,774360373,720215184,719479745,796239200,15182374,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.79643,0.81194,0.25554,0.2603,0.72236,0.72021,0.51775,0.51678,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10401,ERR8516967,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R,0:51 1:51,A:739921027;C:667375549;G:663864111;T:764302396;N:14288091,51,51,,,739921027,667375549,663864111,764302396,14288091,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.90817,0.92909,0.23387,0.24814,0.70088,0.69842,0.51238,0.51267,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 10402,ERR8516968,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X9_190227_A00421_38_AH7523DRXX_S49_R1_001.fastq.gz 15812X9_190227_A00421_38_AH7523DRXX_S49_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X9 190227 A00421 38 AH7523DRXX S49 R,0:51 1:51,A:882831441;C:935213418;G:957033335;T:879085993;N:18444957,51,51,,,882831441,935213418,957033335,879085993,18444957,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.76218,0.7682,0.18357,0.18521,0.74444,0.74272,0.46714,0.55518,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System 24594,SRR25462243,SRX21195038,SRS18453964,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV M3,GSM7669033,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV M3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669033,GSM7669033: PV M3; Danio rerio; RNA Seq,GSM7669033 r1,GSM7669033,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz,fastq fastq,4644457090.0,23465750.0,GSM7669033 r1,0:98.98 1:98.94,A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277,98,98,,,1196567358,1114203322,1109379777,1223156356,1150277,SRX21195038,SRS18453964,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94849,0.95248,0.02727,0.02708,0.73602,0.73718,0.48396,0.4855,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System 24595,SRR25462244,SRX21195037,SRS18453963,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV M2,GSM7669032,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV M2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669032,GSM7669032: PV M2; Danio rerio; RNA Seq,GSM7669032 r1,GSM7669032,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz,fastq fastq,2464506276.0,12449948.0,GSM7669032 r1,0:98.99 1:98.96,A:632587002;C:593372099;G:591579950;T:646214108;N:753117,98,98,,,632587002,593372099,591579950,646214108,753117,SRX21195037,SRS18453963,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94889,0.9522,0.02585,0.02585,0.73669,0.73841,0.48398,0.48486,100,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System 24596,SRR25462245,SRX21195036,SRS18453962,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV M1,GSM7669031,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV M1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669031,GSM7669031: PV M1; Danio rerio; RNA Seq,GSM7669031 r1,GSM7669031,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz,fastq fastq,3634173229.0,18461903.0,GSM7669031 r1,0:98.44 1:98.41,A:930322973;C:875929476;G:875710056;T:948595199;N:3615525,98,98,,,930322973,875929476,875710056,948595199,3615525,SRX21195036,SRS18453962,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94787,0.95134,0.02457,0.02445,0.73762,0.73843,0.48244,0.48069,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System 24597,SRR25462246,SRX21195035,SRS18453961,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV WT3,GSM7669030,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV WT3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669030,GSM7669030: PV WT3; Danio rerio; RNA Seq,GSM7669030 r1,GSM7669030,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT3_R2.fastq PV_WT3_R1.fastq,fastq fastq,2965772270.0,14976621.0,GSM7669030 r1,0:99.03 1:98.99,A:759343389;C:716154246;G:713466520;T:775995980;N:812135,99,98,,,759343389,716154246,713466520,775995980,812135,SRX21195035,SRS18453961,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.95027,0.95485,0.02356,0.02292,0.74422,0.74554,0.47974,0.48267,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System 24598,SRR25462247,SRX21195034,SRS18453960,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV WT2,GSM7669029,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV WT2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669029,GSM7669029: PV WT2; Danio rerio; RNA Seq,GSM7669029 r1,GSM7669029,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT2_R2.fastq PV_WT2_R1.fastq,fastq fastq,2021387268.0,10195384.0,GSM7669029 r1,0:99.15 1:99.12,A:517788644;C:487363563;G:485168383;T:530550229;N:516449,99,99,,,517788644,487363563,485168383,530550229,516449,SRX21195034,SRS18453960,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.95113,0.9544,0.02394,0.02364,0.74168,0.74363,0.47881,0.47499,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System 24599,SRR25462248,SRX21195033,SRS18453959,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV WT1,GSM7669028,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV WT1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669028,GSM7669028: PV WT1; Danio rerio; RNA Seq,GSM7669028 r1,GSM7669028,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT1_R1.fastq PV_WT1_R2.fastq,fastq fastq,3244660111.0,16481925.0,GSM7669028 r1,0:98.44 1:98.42,A:831426044;C:781489498;G:779991004;T:848549246;N:3204319,98,98,,,831426044,781489498,779991004,848549246,3204319,SRX21195033,SRS18453959,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94779,0.95185,0.02328,0.02298,0.74294,0.74391,0.48052,0.47966,95,95,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System 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,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,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,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 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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 3,GSM7812988,,source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing,unDMSO t1 K2 3,Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files,whole embryo,Embryos were exposed to gamma IR of 20 Gy at xxx hpf,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos,tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO,GSM7812988,GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq,GSM7812988 r1,GSM7812988,1,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP463749,,loader:fastq load.py,JON686A36_S54_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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 3,GSM7812988,,source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing,unDMSO t1 K2 3,Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files,whole embryo,Embryos were exposed to gamma IR of 20 Gy at xxx hpf,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos,tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO,GSM7812988,GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq,GSM7812988 r1,GSM7812988,1,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP463749,,loader:fastq load.py,JON686A36_S54_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,SRR26209664,SRX21920659,SRS19005178,SRP463749,PRJNA1022096,Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses,GSE244291,Transcriptome Analysis,The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 3,GSM7812988,,source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing,unDMSO t1 K2 3,Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files,whole embryo,Embryos were exposed to gamma IR of 20 Gy at xxx hpf,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos,tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO,GSM7812988,GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq,GSM7812988 r1,GSM7812988,1,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP463749,,loader:fastq load.py,JON686A36_S54_L007_R1_001.fastq.gz,fastq,596645683.0,5907383.0,GSM7812988 r3,0:101,A:153131508;C:143126741;G:134745614;T:165635953;N:5867,101,,,,153131508,143126741,134745614,165635953,5867,SRX21920659,SRS19005178,SRA1722794,"Devenport, Molecular Biology, Princeton University","Devenport, Molecular Biology, Princeton University",1,0.94156,,0.07795,,0.69751,,0.4833,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,bulk,bulk,,United States,2023-09-28,Undetermined,Embryo,Whole Organism,All anatomical structures 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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 3,GSM7812988,,source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing,unDMSO t1 K2 3,Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files,whole embryo,Embryos were exposed to gamma IR of 20 Gy at xxx hpf,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos,tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO,GSM7812988,GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq,GSM7812988 r1,GSM7812988,1,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP463749,,loader:fastq load.py,JON686A36_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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 3,GSM7812988,,source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing,unDMSO t1 K2 3,Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files,whole embryo,Embryos were exposed to gamma IR of 20 Gy at xxx hpf,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos,tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO,GSM7812988,GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq,GSM7812988 r1,GSM7812988,1,Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP463749,,loader:fastq load.py,JON686A36_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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 K2 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,unDMSO t1 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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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,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 then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control,,pubmed:39437839,,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