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957 rows where devstage_curation = "Undetermined" and technology = "bulk"

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experiment.library_selection 5

devstage_curation_coarse 4

experiment.library_layout 2

technology 1

  • bulk · 957 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

devstage_curation 1

  • Undetermined · 957 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 24652 SRR25487068 SRX21218619 SRS18475798 SRP452670 PRJNA1000968 CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo GSE239788 Transcriptome Analysis Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.   pubmed:38114601   nexn / biological replicate 2 GSM7673294   source name:whole organism|tissue:whole organism|genotype:nexn knockout|geo loc name:missing|collection date:missing nexn / biological replicate 2 Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value whole organism   RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics   tissue:whole organism|genotype:nexn knockout GSM7673294 GSM7673294: nexn / biological replicate 2; Danio rerio; RNA Seq GSM7673294 r1 GSM7673294 1 RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP452670   loader:fastq load.py NG-33220_nexn_E2_mut3_lib700540_10254_1_2.fastq.gz NG-33220_nexn_E2_mut3_lib700540_10254_1_1.fastq.gz fastq fastq 12821226686.0 42454393.0 GSM7673294 r1 0:151 1:151 A:3460123169;C:2958819646;G:3023309404;T:3378893399;N:81068 151 151     3460123169 2958819646 3023309404 3378893399 81068 SRX21218619 SRS18475798 SRA1684694 Molecular Cardiology, Internal Medicine II, Uniklinik Ulm Molecular Cardiology, Internal Medicine II, Uniklinik Ulm 2 0.96544 0.96684 0.07136 0.06827 0.66969 0.66914 0.44957 0.45604 151 151 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk bulk bulk   Germany 2023-08-01 Undetermined Embryo Whole Organism All anatomical structures
24653 24653 SRR25487069 SRX21218618 SRS18475797 SRP452670 PRJNA1000968 CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo GSE239788 Transcriptome Analysis Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.   pubmed:38114601   nexn / biological replicate 1 GSM7673293   source name:whole organism|tissue:whole organism|genotype:nexn knockout|geo loc name:missing|collection date:missing nexn / biological replicate 1 Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value whole organism   RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics   tissue:whole organism|genotype:nexn knockout GSM7673293 GSM7673293: nexn / biological replicate 1; Danio rerio; RNA Seq GSM7673293 r1 GSM7673293 1 RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP452670   loader:fastq load.py NG-33220_nexn_E2_mut1_lib691942_10222_3_2.fastq.gz NG-33220_nexn_E2_mut1_lib691942_10222_3_1.fastq.gz fastq fastq 6518650974.0 21584937.0 GSM7673293 r1 0:151 1:151 A:1776227735;C:1486881610;G:1503672330;T:1751641678;N:227621 151 151     1776227735 1486881610 1503672330 1751641678 227621 SRX21218618 SRS18475797 SRA1684694 Molecular Cardiology, Internal Medicine II, Uniklinik Ulm Molecular Cardiology, Internal Medicine II, Uniklinik Ulm 2 0.9619 0.96365 0.08223 0.07902 0.66967 0.66811 0.44763 0.45022 151 151 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk bulk bulk   Germany 2023-08-01 Undetermined Embryo Whole Organism All anatomical structures
24654 24654 SRR25487070 SRX21218617 SRS18475796 SRP452670 PRJNA1000968 CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo GSE239788 Transcriptome Analysis Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.   pubmed:38114601   nexn+/+ biological replicate 2 GSM7673292   source name:whole organism|tissue:whole organism|genotype:WT|geo loc name:missing|collection date:missing nexn+/+ biological replicate 2 Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value whole organism   RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics   tissue:whole organism|genotype:WT GSM7673292 GSM7673292: nexn+/+ biological replicate 2; Danio rerio; RNA Seq GSM7673292 r1 GSM7673292 1 RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP452670   loader:fastq load.py NG-33220_nexn_E2_sib3_lib693760_10227_1_1.fastq.gz NG-33220_nexn_E2_sib3_lib693760_10227_1_2.fastq.gz fastq fastq 9966559304.0 33001852.0 GSM7673292 r1 0:151 1:151 A:2799666848;C:2201108797;G:2237142072;T:2728542087;N:99500 151 151     2799666848 2201108797 2237142072 2728542087 99500 SRX21218617 SRS18475796 SRA1684694 Molecular Cardiology, Internal Medicine II, Uniklinik Ulm Molecular Cardiology, Internal Medicine II, Uniklinik Ulm 2 0.95433 0.9562 0.11378 0.10948 0.68426 0.68302 0.45622 0.46107 151 151 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk bulk bulk   Germany 2023-08-01 Undetermined Embryo Whole Organism All anatomical structures
24655 24655 SRR25487071 SRX21218616 SRS18475795 SRP452670 PRJNA1000968 CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo GSE239788 Transcriptome Analysis Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.   pubmed:38114601   nexn+/+ biological replicate 1 GSM7673291   source name:whole organism|tissue:whole organism|genotype:WT|geo loc name:missing|collection date:missing nexn+/+ biological replicate 1 Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value whole organism   RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics   tissue:whole organism|genotype:WT GSM7673291 GSM7673291: nexn+/+ biological replicate 1; Danio rerio; RNA Seq GSM7673291 r1 GSM7673291 1 RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP452670   loader:fastq load.py NG-33220_nexn_E2_sib2_lib693759_10227_2_1.fastq.gz NG-33220_nexn_E2_sib2_lib693759_10227_2_2.fastq.gz fastq fastq 13610380470.0 45067485.0 GSM7673291 r1 0:151 1:151 A:3776423931;C:3037607848;G:3100752195;T:3694688167;N:908329 151 151     3776423931 3037607848 3100752195 3694688167 908329 SRX21218616 SRS18475795 SRA1684694 Molecular Cardiology, Internal Medicine II, Uniklinik Ulm Molecular Cardiology, Internal Medicine II, Uniklinik Ulm 2 0.95714 0.95793 0.10127 0.09788 0.69445 0.69278 0.47084 0.46602 151 151 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk bulk bulk   Germany 2023-08-01 Undetermined Embryo Whole Organism All anatomical structures
28113 28113 SRR26209648 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S48_L005_R1_001.fastq.gz fastq 616449359.0 6103459.0 GSM7812991 r1 0:101 A:152808626;C:149738763;G:141639387;T:172257280;N:5303 101       152808626 149738763 141639387 172257280 5303 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94246   0.08766   0.69443   0.4842   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28114 28114 SRR26209649 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S48_L006_R1_001.fastq.gz fastq 609999297.0 6039597.0 GSM7812991 r2 0:101 A:151226657;C:148143193;G:140088806;T:170530812;N:9829 101       151226657 148143193 140088806 170530812 9829 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94201   0.08569   0.69572   0.48692   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28115 28115 SRR26209650 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S48_L007_R1_001.fastq.gz fastq 543730470.0 5383470.0 GSM7812991 r3 0:101 A:134685766;C:132190291;G:124881864;T:151967639;N:4910 101       134685766 132190291 124881864 151967639 4910 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9431   0.08733   0.69524   0.48528   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28116 28116 SRR26209651 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S16_L007_R1_001.fastq.gz fastq 649354149.0 6429249.0 GSM7812991 r4 0:101 A:160756303;C:158145998;G:149623680;T:180816390;N:11778 101       160756303 158145998 149623680 180816390 11778 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94438   0.08618   0.69473   0.48809   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28117 28117 SRR26209752 SRX21920662 SRS19005181 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 3 GSM7812991   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812991 GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq GSM7812991 r1 GSM7812991 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A30_S16_L008_R1_001.fastq.gz fastq 650450504.0 6440104.0 GSM7812991 r5 0:101 A:161054597;C:158340761;G:149784923;T:181251361;N:18862 101       161054597 158340761 149784923 181251361 18862 SRX21920662 SRS19005181 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94338   0.08713   0.6968   0.48443   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28118 28118 SRR26209652 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S46_L005_R1_001.fastq.gz fastq 593068162.0 5871962.0 GSM7812990 r1 0:101 A:147906639;C:143944406;G:137307101;T:163904929;N:5087 101       147906639 143944406 137307101 163904929 5087 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94371   0.06473   0.69378   0.47765   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28119 28119 SRR26209653 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S46_L006_R1_001.fastq.gz fastq 588323081.0 5824981.0 GSM7812990 r2 0:101 A:146630863;C:142829925;G:136124185;T:162728186;N:9922 101       146630863 142829925 136124185 162728186 9922 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94282   0.06357   0.69418   0.47665   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28120 28120 SRR26209654 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S46_L007_R1_001.fastq.gz fastq 521265747.0 5161047.0 GSM7812990 r3 0:101 A:129905878;C:126622019;G:120526207;T:144206853;N:4790 101       129905878 126622019 120526207 144206853 4790 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94508   0.06499   0.69367   0.4834   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28121 28121 SRR26209655 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S26_L007_R1_001.fastq.gz fastq 623834580.0 6176580.0 GSM7812990 r4 0:101 A:155642981;C:151651242;G:144681951;T:171847192;N:11214 101       155642981 151651242 144681951 171847192 11214 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94531   0.06514   0.69225   0.48187   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28122 28122 SRR26209656 SRX21920661 SRS19005180 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 2 GSM7812990   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812990 GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq GSM7812990 r1 GSM7812990 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A29_S26_L008_R1_001.fastq.gz fastq 622155960.0 6159960.0 GSM7812990 r5 0:101 A:155145221;C:151231599;G:144290581;T:171470641;N:17918 101       155145221 151231599 144290581 171470641 17918 SRX21920661 SRS19005180 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94319   0.06413   0.69449   0.48159   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28123 28123 SRR26209657 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S45_L005_R1_001.fastq.gz fastq 602520550.0 5965550.0 GSM7812989 r1 0:101 A:149619230;C:146559346;G:139674646;T:166662143;N:5185 101       149619230 146559346 139674646 166662143 5185 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94449   0.06296   0.69487   0.48   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28124 28124 SRR26209658 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S45_L006_R1_001.fastq.gz fastq 596942522.0 5910322.0 GSM7812989 r2 0:101 A:148193962;C:145221539;G:138267073;T:165249833;N:10115 101       148193962 145221539 138267073 165249833 10115 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9446   0.06327   0.69562   0.48183   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28125 28125 SRR26209659 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S45_L007_R1_001.fastq.gz fastq 532539064.0 5272664.0 GSM7812989 r3 0:101 A:132217323;C:129660296;G:123303893;T:147352732;N:4820 101       132217323 129660296 123303893 147352732 4820 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94579   0.06237   0.69554   0.46658   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28126 28126 SRR26209660 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S29_L007_R1_001.fastq.gz fastq 633337569.0 6270669.0 GSM7812989 r4 0:101 A:157286526;C:154336036;G:147137950;T:174565295;N:11762 101       157286526 154336036 147137950 174565295 11762 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94562   0.06294   0.69489   0.47406   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28127 28127 SRR26209661 SRX21920660 SRS19005179 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 WT 1 GSM7812989   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO GSM7812989 GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq GSM7812989 r1 GSM7812989 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A28_S29_L008_R1_001.fastq.gz fastq 636051540.0 6297540.0 GSM7812989 r5 0:101 A:157845668;C:154972063;G:147765532;T:175449801;N:18476 101       157845668 154972063 147765532 175449801 18476 SRX21920660 SRS19005179 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9471   0.06288   0.69536   0.4797   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28128 28128 SRR26209662 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S54_L005_R1_001.fastq.gz fastq 674188635.0 6675135.0 GSM7812988 r1 0:101 A:173104307;C:161481671;G:152542615;T:187053812;N:6230 101       173104307 161481671 152542615 187053812 6230 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94039   0.07795   0.69877   0.48386   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28129 28129 SRR26209663 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S54_L006_R1_001.fastq.gz fastq 667048339.0 6604439.0 GSM7812988 r2 0:101 A:171316049;C:159786547;G:150743446;T:185190228;N:12069 101       171316049 159786547 150743446 185190228 12069 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94064   0.07881   0.69767   0.48162   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28130 28130 SRR26209664 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S54_L007_R1_001.fastq.gz fastq 596645683.0 5907383.0 GSM7812988 r3 0:101 A:153131508;C:143126741;G:134745614;T:165635953;N:5867 101       153131508 143126741 134745614 165635953 5867 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94156   0.07795   0.69751   0.4833   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28131 28131 SRR26209665 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S12_L007_R1_001.fastq.gz fastq 712385926.0 7053326.0 GSM7812988 r4 0:101 A:183100436;C:171026605;G:161510527;T:196734608;N:13750 101       183100436 171026605 161510527 196734608 13750 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94298   0.07892   0.6997   0.48331   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28132 28132 SRR26209666 SRX21920659 SRS19005178 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 3 GSM7812988   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812988 GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq GSM7812988 r1 GSM7812988 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A36_S12_L008_R1_001.fastq.gz fastq 714661355.0 7075855.0 GSM7812988 r5 0:101 A:183454698;C:171554090;G:162064705;T:197567065;N:20797 101       183454698 171554090 162064705 197567065 20797 SRX21920659 SRS19005178 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94316   0.07877   0.70051   0.48354   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28133 28133 SRR26209667 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S53_L005_R1_001.fastq.gz fastq 611900723.0 6058423.0 GSM7812987 r1 0:101 A:154668392;C:147817141;G:139653400;T:169756342;N:5448 101       154668392 147817141 139653400 169756342 5448 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94636   0.08022   0.69962   0.48201   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28134 28134 SRR26209668 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S53_L006_R1_001.fastq.gz fastq 602971818.0 5970018.0 GSM7812987 r2 0:101 A:152346877;C:145640105;G:137576284;T:167398281;N:10271 101       152346877 145640105 137576284 167398281 10271 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94549   0.08086   0.69781   0.47842   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28135 28135 SRR26209669 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S53_L007_R1_001.fastq.gz fastq 539246575.0 5339075.0 GSM7812987 r3 0:101 A:136317506;C:130390122;G:122927887;T:149606028;N:5032 101       136317506 130390122 122927887 149606028 5032 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94653   0.08075   0.69704   0.48374   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28136 28136 SRR26209670 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S47_L007_R1_001.fastq.gz fastq 643197593.0 6368293.0 GSM7812987 r4 0:101 A:162743675;C:155711536;G:147135700;T:177594459;N:12223 101       162743675 155711536 147135700 177594459 12223 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94757   0.08023   0.70055   0.48458   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28137 28137 SRR26209671 SRX21920658 SRS19005177 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 2 GSM7812987   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812987 GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq GSM7812987 r1 GSM7812987 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A35_S47_L008_R1_001.fastq.gz fastq 644356063.0 6379763.0 GSM7812987 r5 0:101 A:162915651;C:155935181;G:147406641;T:178079118;N:19472 101       162915651 155935181 147406641 178079118 19472 SRX21920658 SRS19005177 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94817   0.08218   0.70017   0.48286   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28138 28138 SRR26209672 SRX21920657 SRS19005176 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 1 GSM7812986   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812986 GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq GSM7812986 r1 GSM7812986 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A34_S52_L005_R1_001.fastq.gz fastq 615996374.0 6098974.0 GSM7812986 r1 0:101 A:156934542;C:147417998;G:139301915;T:172336421;N:5498 101       156934542 147417998 139301915 172336421 5498 SRX21920657 SRS19005176 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94179   0.07628   0.69512   0.48041   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28139 28139 SRR26209673 SRX21920657 SRS19005176 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 1 GSM7812986   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812986 GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq GSM7812986 r1 GSM7812986 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A34_S52_L006_R1_001.fastq.gz fastq 608875571.0 6028471.0 GSM7812986 r2 0:101 A:155127967;C:145701864;G:137575885;T:170459017;N:10838 101       155127967 145701864 137575885 170459017 10838 SRX21920657 SRS19005176 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94248   0.07563   0.69512   0.47982   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28140 28140 SRR26209674 SRX21920657 SRS19005176 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 1 GSM7812986   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812986 GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq GSM7812986 r1 GSM7812986 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A34_S52_L007_R1_001.fastq.gz fastq 539739455.0 5343955.0 GSM7812986 r3 0:101 A:137431217;C:129328124;G:121891472;T:151083373;N:5269 101       137431217 129328124 121891472 151083373 5269 SRX21920657 SRS19005176 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9438   0.07511   0.69654   0.48083   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28141 28141 SRR26209675 SRX21920657 SRS19005176 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 1 GSM7812986   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812986 GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq GSM7812986 r1 GSM7812986 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A34_S65_L007_R1_001.fastq.gz fastq 648984489.0 6425589.0 GSM7812986 r4 0:101 A:165552674;C:155580501;G:147078092;T:180761105;N:12117 101       165552674 155580501 147078092 180761105 12117 SRX21920657 SRS19005176 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94513   0.07694   0.69451   0.48174   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28142 28142 SRR26209676 SRX21920657 SRS19005176 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K2 1 GSM7812986   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K2 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO GSM7812986 GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq GSM7812986 r1 GSM7812986 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A34_S65_L008_R1_001.fastq.gz fastq 651988330.0 6455330.0 GSM7812986 r5 0:101 A:166130853;C:156282200;G:147738788;T:181817695;N:18794 101       166130853 156282200 147738788 181817695 18794 SRX21920657 SRS19005176 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94437   0.0759   0.69597   0.48083   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28143 28143 SRR26209677 SRX21920656 SRS19005175 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 3 GSM7812985   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812985 GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq GSM7812985 r1 GSM7812985 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A33_S51_L005_R1_001.fastq.gz fastq 621669544.0 6155144.0 GSM7812985 r1 0:101 A:157346917;C:148083763;G:141122336;T:175110946;N:5582 101       157346917 148083763 141122336 175110946 5582 SRX21920656 SRS19005175 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94207   0.06859   0.69473   0.48838   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28144 28144 SRR26209678 SRX21920656 SRS19005175 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 3 GSM7812985   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812985 GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq GSM7812985 r1 GSM7812985 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A33_S51_L006_R1_001.fastq.gz fastq 613437842.0 6073642.0 GSM7812985 r2 0:101 A:155200714;C:146135271;G:139223090;T:172868018;N:10749 101       155200714 146135271 139223090 172868018 10749 SRX21920656 SRS19005175 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94144   0.06885   0.69471   0.48996   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28145 28145 SRR26209679 SRX21920656 SRS19005175 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 3 GSM7812985   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812985 GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq GSM7812985 r1 GSM7812985 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A33_S51_L007_R1_001.fastq.gz fastq 546684518.0 5412718.0 GSM7812985 r3 0:101 A:138292090;C:130364936;G:123978492;T:154043685;N:5315 101       138292090 130364936 123978492 154043685 5315 SRX21920656 SRS19005175 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94375   0.06988   0.69589   0.48741   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28146 28146 SRR26209680 SRX21920656 SRS19005175 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 3 GSM7812985   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812985 GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq GSM7812985 r1 GSM7812985 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A33_S43_L007_R1_001.fastq.gz fastq 651065089.0 6446189.0 GSM7812985 r4 0:101 A:164874330;C:155389435;G:148130531;T:182658473;N:12320 101       164874330 155389435 148130531 182658473 12320 SRX21920656 SRS19005175 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94247   0.06954   0.69538   0.48283   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28147 28147 SRR26209681 SRX21920656 SRS19005175 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 3 GSM7812985   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812985 GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq GSM7812985 r1 GSM7812985 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A33_S43_L008_R1_001.fastq.gz fastq 652838952.0 6463752.0 GSM7812985 r5 0:101 A:165235507;C:155756581;G:148483290;T:183344035;N:19539 101       165235507 155756581 148483290 183344035 19539 SRX21920656 SRS19005175 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94297   0.06917   0.69593   0.4827   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28148 28148 SRR26209682 SRX21920655 SRS19005174 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 2 GSM7812984   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812984 GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq GSM7812984 r1 GSM7812984 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A32_S50_L005_R1_001.fastq.gz fastq 531938215.0 5266715.0 GSM7812984 r1 0:101 A:131083905;C:128715617;G:122601298;T:149532970;N:4425 101       131083905 128715617 122601298 149532970 4425 SRX21920655 SRS19005174 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94249   0.07108   0.69485   0.47386   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28149 28149 SRR26209683 SRX21920655 SRS19005174 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 2 GSM7812984   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812984 GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq GSM7812984 r1 GSM7812984 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A32_S50_L006_R1_001.fastq.gz fastq 527781863.0 5225563.0 GSM7812984 r2 0:101 A:130119726;C:127646784;G:121549831;T:148456993;N:8529 101       130119726 127646784 121549831 148456993 8529 SRX21920655 SRS19005174 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94199   0.0713   0.69337   0.473   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28150 28150 SRR26209684 SRX21920655 SRS19005174 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 2 GSM7812984   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812984 GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq GSM7812984 r1 GSM7812984 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A32_S50_L007_R1_001.fastq.gz fastq 472785040.0 4681040.0 GSM7812984 r3 0:101 A:116503463;C:114489771;G:108989839;T:132797698;N:4269 101       116503463 114489771 108989839 132797698 4269 SRX21920655 SRS19005174 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94373   0.07285   0.69467   0.47913   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28151 28151 SRR26209685 SRX21920655 SRS19005174 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 2 GSM7812984   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812984 GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq GSM7812984 r1 GSM7812984 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A32_S71_L007_R1_001.fastq.gz fastq 561056414.0 5555014.0 GSM7812984 r4 0:101 A:138240115;C:136040813;G:129592563;T:157172399;N:10524 101       138240115 136040813 129592563 157172399 10524 SRX21920655 SRS19005174 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94357   0.07109   0.69544   0.47169   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28152 28152 SRR26209686 SRX21920655 SRS19005174 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 2 GSM7812984   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812984 GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq GSM7812984 r1 GSM7812984 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A32_S71_L008_R1_001.fastq.gz fastq 563109744.0 5575344.0 GSM7812984 r5 0:101 A:138778764;C:136444809;G:129964766;T:157904708;N:16697 101       138778764 136444809 129964766 157904708 16697 SRX21920655 SRS19005174 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94358   0.07253   0.69345   0.47443   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28153 28153 SRR26209687 SRX21920654 SRS19005173 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 1 GSM7812983   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812983 GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq GSM7812983 r1 GSM7812983 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A31_S49_L005_R1_001.fastq.gz fastq 576725857.0 5710157.0 GSM7812983 r1 0:101 A:142557020;C:140092748;G:133378036;T:160693137;N:4916 101       142557020 140092748 133378036 160693137 4916 SRX21920654 SRS19005173 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94239   0.07259   0.69398   0.47675   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28154 28154 SRR26209688 SRX21920654 SRS19005173 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 1 GSM7812983   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812983 GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq GSM7812983 r1 GSM7812983 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A31_S49_L006_R1_001.fastq.gz fastq 569166310.0 5635310.0 GSM7812983 r2 0:101 A:140702145;C:138232540;G:131558917;T:158663414;N:9294 101       140702145 138232540 131558917 158663414 9294 SRX21920654 SRS19005173 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94221   0.07252   0.69524   0.4833   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28155 28155 SRR26209689 SRX21920654 SRS19005173 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 1 GSM7812983   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812983 GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq GSM7812983 r1 GSM7812983 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A31_S49_L007_R1_001.fastq.gz fastq 505699425.0 5006925.0 GSM7812983 r3 0:101 A:124940125;C:122891114;G:116919354;T:140944307;N:4525 101       124940125 122891114 116919354 140944307 4525 SRX21920654 SRS19005173 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.944   0.07242   0.69473   0.48289   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28156 28156 SRR26209690 SRX21920654 SRS19005173 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 1 GSM7812983   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812983 GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq GSM7812983 r1 GSM7812983 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A31_S27_L007_R1_001.fastq.gz fastq 598624374.0 5926974.0 GSM7812983 r4 0:101 A:147863525;C:145723385;G:138724140;T:166302217;N:11107 101       147863525 145723385 138724140 166302217 11107 SRX21920654 SRS19005173 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94426   0.07312   0.69479   0.48056   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28157 28157 SRR26209691 SRX21920654 SRS19005173 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   unDMSO t1 K1 1 GSM7812983   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing unDMSO t1 K1 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO GSM7812983 GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq GSM7812983 r1 GSM7812983 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A31_S27_L008_R1_001.fastq.gz fastq 602654072.0 5966872.0 GSM7812983 r5 0:101 A:148869054;C:146693906;G:139571739;T:167501958;N:17415 101       148869054 146693906 139571739 167501958 17415 SRX21920654 SRS19005173 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9433   0.0732   0.69552   0.47807   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28158 28158 SRR26209692 SRX21920653 SRS19005172 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 3 GSM7812982   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812982 GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq GSM7812982 r1 GSM7812982 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A21_S38_L005_R1_001.fastq.gz fastq 617990619.0 6118719.0 GSM7812982 r1 0:101 A:155764078;C:148642484;G:140551460;T:173027146;N:5451 101       155764078 148642484 140551460 173027146 5451 SRX21920653 SRS19005172 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93982   0.07316   0.68801   0.48964   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28159 28159 SRR26209693 SRX21920653 SRS19005172 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 3 GSM7812982   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812982 GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq GSM7812982 r1 GSM7812982 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A21_S38_L006_R1_001.fastq.gz fastq 612677312.0 6066112.0 GSM7812982 r2 0:101 A:154425053;C:147379484;G:139208932;T:171653577;N:10266 101       154425053 147379484 139208932 171653577 10266 SRX21920653 SRS19005172 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93954   0.07439   0.68945   0.48768   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28160 28160 SRR26209694 SRX21920653 SRS19005172 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 3 GSM7812982   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812982 GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq GSM7812982 r1 GSM7812982 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A21_S38_L007_R1_001.fastq.gz fastq 545311221.0 5399121.0 GSM7812982 r3 0:101 A:137422024;C:131281461;G:123803444;T:152799164;N:5128 101       137422024 131281461 123803444 152799164 5128 SRX21920653 SRS19005172 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94119   0.07433   0.6886   0.48763   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28161 28161 SRR26209695 SRX21920653 SRS19005172 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 3 GSM7812982   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812982 GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq GSM7812982 r1 GSM7812982 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A21_S68_L007_R1_001.fastq.gz fastq 643233246.0 6368646.0 GSM7812982 r4 0:101 A:162062613;C:155064589;G:146625670;T:179468362;N:12012 101       162062613 155064589 146625670 179468362 12012 SRX21920653 SRS19005172 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94076   0.07335   0.68747   0.48953   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28162 28162 SRR26209696 SRX21920653 SRS19005172 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 3 GSM7812982   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812982 GSM7812982: IR t2 WT 3; Danio rerio; RNA Seq GSM7812982 r1 GSM7812982 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A21_S68_L008_R1_001.fastq.gz fastq 643010339.0 6366439.0 GSM7812982 r5 0:101 A:161939065;C:154897858;G:146526716;T:179627762;N:18938 101       161939065 154897858 146526716 179627762 18938 SRX21920653 SRS19005172 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94077   0.07428   0.68852   0.4878   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28163 28163 SRR26209697 SRX21920652 SRS19005171 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 2 GSM7812981   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812981 GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq GSM7812981 r1 GSM7812981 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A20_S37_L005_R1_001.fastq.gz fastq 608303002.0 6022802.0 GSM7812981 r1 0:101 A:151266125;C:146608795;G:139308397;T:171114479;N:5206 101       151266125 146608795 139308397 171114479 5206 SRX21920652 SRS19005171 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9409   0.06934   0.68702   0.48691   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28164 28164 SRR26209698 SRX21920652 SRS19005171 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 2 GSM7812981   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812981 GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq GSM7812981 r1 GSM7812981 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A20_S37_L006_R1_001.fastq.gz fastq 602278857.0 5963157.0 GSM7812981 r2 0:101 A:149885037;C:145060278;G:137831227;T:169492101;N:10214 101       149885037 145060278 137831227 169492101 10214 SRX21920652 SRS19005171 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94168   0.06967   0.68491   0.48684   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28165 28165 SRR26209699 SRX21920652 SRS19005171 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 2 GSM7812981   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812981 GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq GSM7812981 r1 GSM7812981 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A20_S37_L007_R1_001.fastq.gz fastq 539699863.0 5343563.0 GSM7812981 r3 0:101 A:134101752;C:130207416;G:123553593;T:151832349;N:4753 101       134101752 130207416 123553593 151832349 4753 SRX21920652 SRS19005171 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94262   0.06995   0.68605   0.48097   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28166 28166 SRR26209700 SRX21920652 SRS19005171 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 2 GSM7812981   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812981 GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq GSM7812981 r1 GSM7812981 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A20_S13_L007_R1_001.fastq.gz fastq 629529263.0 6232963.0 GSM7812981 r4 0:101 A:156345013;C:152106432;G:144536894;T:176529480;N:11444 101       156345013 152106432 144536894 176529480 11444 SRX21920652 SRS19005171 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94267   0.06864   0.68477   0.47912   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28167 28167 SRR26209701 SRX21920652 SRS19005171 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   IR t2 WT 2 GSM7812981   source name:whole embryo|tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR|geo loc name:missing|collection date:missing IR t2 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t2|genotype:WT|treatment:IR GSM7812981 GSM7812981: IR t2 WT 2; Danio rerio; RNA Seq GSM7812981 r1 GSM7812981 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A20_S13_L008_R1_001.fastq.gz fastq 633828732.0 6275532.0 GSM7812981 r5 0:101 A:157411401;C:153033686;G:145422340;T:177942918;N:18387 101       157411401 153033686 145422340 177942918 18387 SRX21920652 SRS19005171 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94386   0.06993   0.68479   0.48216   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28168 28168 SRR26209702 SRX21920651 SRS19005170 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 3 GSM7813000   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7813000 GSM7813000: un t1 WT 3; Danio rerio; RNA Seq GSM7813000 r1 GSM7813000 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A3_S47_L005_R1_001.fastq.gz fastq 576015423.0 5703123.0 GSM7813000 r1 0:101 A:142483427;C:134492274;G:128574929;T:170459571;N:5222 101       142483427 134492274 128574929 170459571 5222 SRX21920651 SRS19005170 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93576   0.07681   0.6939   0.4794   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28169 28169 SRR26209703 SRX21920651 SRS19005170 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 3 GSM7813000   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7813000 GSM7813000: un t1 WT 3; Danio rerio; RNA Seq GSM7813000 r1 GSM7813000 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A3_S47_L006_R1_001.fastq.gz fastq 568813012.0 5631812.0 GSM7813000 r2 0:101 A:140699035;C:132793802;G:126863421;T:168447319;N:9435 101       140699035 132793802 126863421 168447319 9435 SRX21920651 SRS19005170 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93455   0.07506   0.69229   0.47926   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28170 28170 SRR26209704 SRX21920651 SRS19005170 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 3 GSM7813000   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7813000 GSM7813000: un t1 WT 3; Danio rerio; RNA Seq GSM7813000 r1 GSM7813000 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A3_S47_L007_R1_001.fastq.gz fastq 510666908.0 5056108.0 GSM7813000 r3 0:101 A:126264547;C:119308486;G:114018656;T:151070721;N:4498 101       126264547 119308486 114018656 151070721 4498 SRX21920651 SRS19005170 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93621   0.07582   0.6928   0.48424   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28171 28171 SRR26209705 SRX21920651 SRS19005170 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 3 GSM7813000   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7813000 GSM7813000: un t1 WT 3; Danio rerio; RNA Seq GSM7813000 r1 GSM7813000 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A3_S5_L007_R1_001.fastq.gz fastq 602866980.0 5968980.0 GSM7813000 r4 0:101 A:148987273;C:141267314;G:134805122;T:177796181;N:11090 101       148987273 141267314 134805122 177796181 11090 SRX21920651 SRS19005170 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93771   0.07611   0.69305   0.48012   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28172 28172 SRR26209706 SRX21920651 SRS19005170 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 3 GSM7813000   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7813000 GSM7813000: un t1 WT 3; Danio rerio; RNA Seq GSM7813000 r1 GSM7813000 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A3_S5_L008_R1_001.fastq.gz fastq 605447934.0 5994534.0 GSM7813000 r5 0:101 A:149696103;C:141763945;G:135323063;T:178646888;N:17935 101       149696103 141763945 135323063 178646888 17935 SRX21920651 SRS19005170 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93786   0.0763   0.6911   0.48344   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28173 28173 SRR26209709 SRX21920650 SRS19005168 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 2 GSM7812999   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812999 GSM7812999: un t1 WT 2; Danio rerio; RNA Seq GSM7812999 r1 GSM7812999 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A2_S36_L005_R1_001.fastq.gz fastq 556466166.0 5509566.0 GSM7812999 r1 0:101 A:139611141;C:131729703;G:125284158;T:159836124;N:5040 101       139611141 131729703 125284158 159836124 5040 SRX21920650 SRS19005168 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93631   0.07619   0.69016   0.47322   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28174 28174 SRR26209710 SRX21920650 SRS19005168 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 2 GSM7812999   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812999 GSM7812999: un t1 WT 2; Danio rerio; RNA Seq GSM7812999 r1 GSM7812999 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A2_S36_L006_R1_001.fastq.gz fastq 550955707.0 5455007.0 GSM7812999 r2 0:101 A:138283185;C:130378801;G:123913867;T:158370327;N:9527 101       138283185 130378801 123913867 158370327 9527 SRX21920650 SRS19005168 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93674   0.07558   0.69018   0.47446   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28175 28175 SRR26209711 SRX21920650 SRS19005168 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 2 GSM7812999   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812999 GSM7812999: un t1 WT 2; Danio rerio; RNA Seq GSM7812999 r1 GSM7812999 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A2_S36_L007_R1_001.fastq.gz fastq 489105125.0 4842625.0 GSM7812999 r3 0:101 A:122641903;C:115831859;G:110132706;T:140494104;N:4553 101       122641903 115831859 110132706 140494104 4553 SRX21920650 SRS19005168 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93871   0.07529   0.69067   0.47657   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28176 28176 SRR26209712 SRX21920650 SRS19005168 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 2 GSM7812999   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812999 GSM7812999: un t1 WT 2; Danio rerio; RNA Seq GSM7812999 r1 GSM7812999 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A2_S52_L007_R1_001.fastq.gz fastq 584149862.0 5783662.0 GSM7812999 r4 0:101 A:146448684;C:138570019;G:131766472;T:167353726;N:10961 101       146448684 138570019 131766472 167353726 10961 SRX21920650 SRS19005168 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93862   0.07597   0.69037   0.47425   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28177 28177 SRR26209713 SRX21920650 SRS19005168 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 2 GSM7812999   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812999 GSM7812999: un t1 WT 2; Danio rerio; RNA Seq GSM7812999 r1 GSM7812999 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A2_S52_L008_R1_001.fastq.gz fastq 587223595.0 5814095.0 GSM7812999 r5 0:101 A:147280051;C:139251420;G:132358015;T:168316824;N:17285 101       147280051 139251420 132358015 168316824 17285 SRX21920650 SRS19005168 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93908   0.07566   0.69051   0.47457   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28178 28178 SRR26209714 SRX21920649 SRS19005169 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 1 GSM7812998   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812998 GSM7812998: un t1 WT 1; Danio rerio; RNA Seq GSM7812998 r1 GSM7812998 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A1_S25_L005_R1_001.fastq.gz fastq 586786669.0 5809769.0 GSM7812998 r1 0:101 A:146663914;C:138395633;G:131925721;T:169796344;N:5057 101       146663914 138395633 131925721 169796344 5057 SRX21920649 SRS19005169 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93799   0.0785   0.68921   0.47635   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28179 28179 SRR26209715 SRX21920649 SRS19005169 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 1 GSM7812998   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812998 GSM7812998: un t1 WT 1; Danio rerio; RNA Seq GSM7812998 r1 GSM7812998 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A1_S25_L006_R1_001.fastq.gz fastq 580037142.0 5742942.0 GSM7812998 r2 0:101 A:145023616;C:136736616;G:130314515;T:167952749;N:9646 101       145023616 136736616 130314515 167952749 9646 SRX21920649 SRS19005169 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9375   0.0778   0.69126   0.4693   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28180 28180 SRR26209716 SRX21920649 SRS19005169 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 1 GSM7812998   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812998 GSM7812998: un t1 WT 1; Danio rerio; RNA Seq GSM7812998 r1 GSM7812998 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A1_S25_L007_R1_001.fastq.gz fastq 520166160.0 5150160.0 GSM7812998 r3 0:101 A:129930970;C:122767131;G:117052309;T:150411128;N:4622 101       129930970 122767131 117052309 150411128 4622 SRX21920649 SRS19005169 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93856   0.07769   0.68986   0.47872   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28181 28181 SRR26209717 SRX21920649 SRS19005169 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 1 GSM7812998   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812998 GSM7812998: un t1 WT 1; Danio rerio; RNA Seq GSM7812998 r1 GSM7812998 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A1_S38_L007_R1_001.fastq.gz fastq 613687716.0 6076116.0 GSM7812998 r4 0:101 A:153144671;C:145096423;G:138249991;T:177185506;N:11125 101       153144671 145096423 138249991 177185506 11125 SRX21920649 SRS19005169 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93852   0.07714   0.69114   0.47286   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28182 28182 SRR26209718 SRX21920649 SRS19005169 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 WT 1 GSM7812998   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un|geo loc name:missing|collection date:missing un t1 WT 1 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:WT|treatment:un GSM7812998 GSM7812998: un t1 WT 1; Danio rerio; RNA Seq GSM7812998 r1 GSM7812998 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A1_S38_L008_R1_001.fastq.gz fastq 616318665.0 6102165.0 GSM7812998 r5 0:101 A:153949045;C:145626513;G:138751875;T:177973081;N:18151 101       153949045 145626513 138751875 177973081 18151 SRX21920649 SRS19005169 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93903   0.07786   0.68988   0.47636   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28183 28183 SRR26209719 SRX21920648 SRS19005167 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 K2 3 GSM7812997   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing un t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un GSM7812997 GSM7812997: un t1 K2 3; Danio rerio; RNA Seq GSM7812997 r1 GSM7812997 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A9_S78_L005_R1_001.fastq.gz fastq 724244336.0 7170736.0 GSM7812997 r1 0:101 A:186549355;C:171075233;G:162480404;T:204132811;N:6533 101       186549355 171075233 162480404 204132811 6533 SRX21920648 SRS19005167 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93859   0.0781   0.69398   0.47368   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28184 28184 SRR26209720 SRX21920648 SRS19005167 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 K2 3 GSM7812997   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing un t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un GSM7812997 GSM7812997: un t1 K2 3; Danio rerio; RNA Seq GSM7812997 r1 GSM7812997 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A9_S78_L006_R1_001.fastq.gz fastq 715170900.0 7080900.0 GSM7812997 r2 0:101 A:184237250;C:168924034;G:160306739;T:201690849;N:12028 101       184237250 168924034 160306739 201690849 12028 SRX21920648 SRS19005167 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9387   0.07758   0.69351   0.47477   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28185 28185 SRR26209721 SRX21920648 SRS19005167 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 K2 3 GSM7812997   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing un t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un GSM7812997 GSM7812997: un t1 K2 3; Danio rerio; RNA Seq GSM7812997 r1 GSM7812997 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A9_S78_L007_R1_001.fastq.gz fastq 640321517.0 6339817.0 GSM7812997 r3 0:101 A:164839141;C:151424251;G:143417815;T:180634187;N:6123 101       164839141 151424251 143417815 180634187 6123 SRX21920648 SRS19005167 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93922   0.07776   0.69704   0.47799   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28186 28186 SRR26209722 SRX21920648 SRS19005167 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 K2 3 GSM7812997   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing un t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un GSM7812997 GSM7812997: un t1 K2 3; Danio rerio; RNA Seq GSM7812997 r1 GSM7812997 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A9_S40_L007_R1_001.fastq.gz fastq 761823507.0 7542807.0 GSM7812997 r4 0:101 A:196286252;C:180257625;G:171369071;T:213896271;N:14288 101       196286252 180257625 171369071 213896271 14288 SRX21920648 SRS19005167 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.9401   0.07711   0.69432   0.47434   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28187 28187 SRR26209723 SRX21920648 SRS19005167 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 K2 3 GSM7812997   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing un t1 K2 3 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un GSM7812997 GSM7812997: un t1 K2 3; Danio rerio; RNA Seq GSM7812997 r1 GSM7812997 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A9_S40_L008_R1_001.fastq.gz fastq 766290434.0 7587034.0 GSM7812997 r5 0:101 A:197350392;C:181234905;G:172326999;T:215355106;N:23032 101       197350392 181234905 172326999 215355106 23032 SRX21920648 SRS19005167 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.94063   0.07837   0.69286   0.47547   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28188 28188 SRR26209724 SRX21920647 SRS19005166 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 K2 2 GSM7812996   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing un t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un GSM7812996 GSM7812996: un t1 K2 2; Danio rerio; RNA Seq GSM7812996 r1 GSM7812996 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A8_S77_L005_R1_001.fastq.gz fastq 593569122.0 5876922.0 GSM7812996 r1 0:101 A:149278073;C:141195461;G:134126340;T:168963965;N:5283 101       149278073 141195461 134126340 168963965 5283 SRX21920647 SRS19005166 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93767   0.07505   0.69146   0.4769   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28189 28189 SRR26209725 SRX21920647 SRS19005166 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 K2 2 GSM7812996   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing un t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un GSM7812996 GSM7812996: un t1 K2 2; Danio rerio; RNA Seq GSM7812996 r1 GSM7812996 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A8_S77_L006_R1_001.fastq.gz fastq 589735768.0 5838968.0 GSM7812996 r2 0:101 A:148392810;C:140188863;G:133132306;T:168011761;N:10028 101       148392810 140188863 133132306 168011761 10028 SRX21920647 SRS19005166 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93804   0.07637   0.69112   0.47875   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures
28190 28190 SRR26209726 SRX21920647 SRS19005166 SRP463749 PRJNA1022096 Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses GSE244291 Transcriptome Analysis The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th…   pubmed:39437839   un t1 K2 2 GSM7812996   source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un|geo loc name:missing|collection date:missing un t1 K2 2 Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files whole embryo Embryos were exposed to gamma IR of 20 Gy at xxx hpf Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos tissue:whole embryo|timepoint:t1|genotype:K2|treatment:un GSM7812996 GSM7812996: un t1 K2 2; Danio rerio; RNA Seq GSM7812996 r1 GSM7812996 1 Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP463749   loader:fastq load.py JON686A8_S77_L007_R1_001.fastq.gz fastq 527272217.0 5220517.0 GSM7812996 r3 0:101 A:132562535;C:125471545;G:119166731;T:150066425;N:4981 101       132562535 125471545 119166731 150066425 4981 SRX21920647 SRS19005166 SRA1722794 Devenport, Molecular Biology, Princeton University Devenport, Molecular Biology, Princeton University 1 0.93967   0.07529   0.69138   0.47674   101   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk bulk bulk   United States 2023-09-28 Undetermined Embryo Whole Organism All anatomical structures

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