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1,831 rows where devstage_curation = "Undetermined" and experiment.library_layout = "SINGLE"

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tissue_curation >10

experiment.library_selection >10

technology 8

experiment.library_strategy 7

experiment.platform 6

devstage_curation_coarse 5

experiment.library_source 3

experiment.library_layout 1

  • SINGLE · 1,831 ✖

devstage_curation 1

  • Undetermined · 1,831 ✖
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
62 62 DRR032762 DRX029568 DRS049967 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr prime5 6 3 SAMD00028159   sample name:Dr prime5 6 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028159 DRX029568 Dr prime5 6 3 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028159       3903332800.0 39033328.0 DRR032762 0:100 1:0 A:1050045822;C:908538410;G:900588661;T:1044116537;N:43370 100 0     1050045822 908538410 900588661 1044116537 43370 DRX029568 DRS049967 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92761   0.07976   0.69126   0.46568   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
63 63 DRR032761 DRX029567 DRS049966 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr prime5 6 2 SAMD00028158   sample name:Dr prime5 6 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028158 DRX029567 Dr prime5 6 2 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028158       3678549700.0 36785497.0 DRR032761 0:100 1:0 A:986526644;C:857762765;G:853417738;T:980801764;N:40789 100 0     986526644 857762765 853417738 980801764 40789 DRX029567 DRS049966 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92689   0.07872   0.6928   0.46577   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
64 64 DRR032760 DRX029566 DRS049965 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr prime5 6 1 SAMD00028157   sample name:Dr prime5 6 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028157 DRX029566 Dr prime5 6 1 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028157       3863129500.0 38631295.0 DRR032760 0:100 1:0 A:1035240477;C:901625010;G:895370149;T:1030851937;N:41927 100 0     1035240477 901625010 895370149 1030851937 41927 DRX029566 DRS049965 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92337   0.07522   0.69315   0.46516   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
65 65 DRR032759 DRX029565 DRS049964 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr prime25 2 SAMD00028156   sample name:Dr prime25 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime25|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028156 DRX029565 Dr prime25 2 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028156       3750136100.0 37501361.0 DRR032759 0:100 1:0 A:1013528040;C:866734984;G:862431819;T:1007403208;N:38049 100 0     1013528040 866734984 862431819 1007403208 38049 DRX029565 DRS049964 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92019   0.09079   0.68304   0.47083   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
66 66 DRR032758 DRX029564 DRS049963 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr prime25 1 SAMD00028155   sample name:Dr prime25 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime25|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028155 DRX029564 Dr prime25 1 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028155       3544862700.0 35448627.0 DRR032758 0:100 1:0 A:952135895;C:825841753;G:821757889;T:945087927;N:39236 100 0     952135895 825841753 821757889 945087927 39236 DRX029564 DRS049963 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92229   0.08344   0.68525   0.466   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
67 67 DRR032757 DRX029563 DRS049962 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 97 individuals Dr bud 2 SAMD00028154   sample name:Dr bud 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:bud|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028154 DRX029563 Dr bud 2 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028154       4104778200.0 41047782.0 DRR032757 0:100 1:0 A:1116316188;C:944738800;G:936257056;T:1107423486;N:42670 100 0     1116316188 944738800 936257056 1107423486 42670 DRX029563 DRS049962 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92945   0.10493   0.73407   0.47824   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
68 68 DRR032756 DRX029562 DRS049961 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 100 individuals Dr bud 1 SAMD00028153   sample name:Dr bud 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:bud|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028153 DRX029562 Dr bud 1 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028153       4540291000.0 45402910.0 DRR032756 0:100 1:0 A:1237914068;C:1042346110;G:1033172731;T:1226799791;N:58300 100 0     1237914068 1042346110 1033172731 1226799791 58300 DRX029562 DRS049961 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92628   0.10478   0.7391   0.46461   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
95 95 DRR050167 DRX045209 DRS025834 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 3 SAMD00044057   sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044057 DRX045209 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044057       371748120.0 3469843.0 DRR050167 0:107.14 A:107190409;C:79475572;G:83520360;T:101561779;N:0 107       107190409 79475572 83520360 101561779 0 DRX045209 DRS025834 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.81026   0.26715   0.86953   0.52321   51   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
96 96 DRR050166 DRX045208 DRS025833 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 2 SAMD00044056   sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044056 DRX045208 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044056       425549011.0 3275261.0 DRR050166 0:129.93 A:126640704;C:86415371;G:90822163;T:121670773;N:0 129       126640704 86415371 90822163 121670773 0 DRX045208 DRS025833 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.80223   0.31429   0.85861   0.5272   57   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
97 97 DRR050165 DRX045207 DRS025832 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 1 SAMD00044055   sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044055 DRX045207 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044055       584599765.0 3941083.0 DRR050165 0:148.33 A:164329030;C:129885620;G:136727379;T:153657736;N:0 148       164329030 129885620 136727379 153657736 0 DRX045207 DRS025832 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.83769   0.25395   0.83116   0.52784   185   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
98 98 DRR050164 DRX045206 DRS025831 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 3 SAMD00044054   sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044054 DRX045206 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044054       343014114.0 3827762.0 DRR050164 0:89.61 A:99421434;C:73070267;G:77738821;T:92783592;N:0 89       99421434 73070267 77738821 92783592 0 DRX045206 DRS025831 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.78953   0.25529   0.87367   0.52148   24   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
99 99 DRR050163 DRX045205 DRS025830 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 2 SAMD00044053   sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044053 DRX045205 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044053       533069427.0 3824140.0 DRR050163 0:139.40 A:152608173;C:113928273;G:120051739;T:146481242;N:0 139       152608173 113928273 120051739 146481242 0 DRX045205 DRS025830 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.80412   0.26768   0.85338   0.52255   245   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
100 100 DRR050162 DRX045204 DRS025829 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 1 SAMD00044052   sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044052 DRX045204 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044052       478262965.0 4224064.0 DRR050162 0:113.22 A:136348264;C:104872341;G:113114502;T:123927858;N:0 113       136348264 104872341 113114502 123927858 0 DRX045204 DRS025829 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.86947   0.29839   0.83317   0.51453   80   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
9918 9918 ERR5059480 ERX4865549 ERS5523939 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     aAM 6h rep1 JD AD30 PRPN1970901   ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AD30_PRPN197090.tar.gz nanopore 3739882337.0 3148027.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 0:1188.01 A:1054501690;C:834193435;G:847423060;T:1003764152;N:0 1188       1054501690 834193435 847423060 1003764152 0 ERX4865549 ERS5523939 ERA3206712 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9920 9920 ERR4330695 ERX4277529 ERS4811113 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 2h rep1 WT 2h rep1 SAMEA7050483 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-B2_PDBN005727.tar.gz fastq     ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1                       ERX4277529   ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9921 9921 ERR4327134 ERX4273968 ERS4808634 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep2 WT 4h rep2 SAMEA7048000 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AM39_PDBN042841.tar.gz nanopore 719646261.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 0:801.59 A:210217908;C:152963718;G:157393834;T:199070801;N:0 801       210217908 152963718 157393834 199070801 0 ERX4273968 ERS4808634 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9922 9922 ERR4330696 ERX4277530 ERS4811114 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep1 WT 4h rep1 JD C3 PDBN006177   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-C3_PDBN006177.tar.gz nanopore 4240799932.0 4331689.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 0:979.02 A:1229803846;C:914476674;G:943703560;T:1152815852;N:0 979       1229803846 914476674 943703560 1152815852 0 ERX4277530 ERS4811114 ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9923 9923 ERR4327135 ERX4273969 ERS4808635 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep1 WT 6h rep1 JD AC29 PDBN024889   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AC29_PDBN024889.tar.gz nanopore 1900324756.0 2013035.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 0:944.01 A:549431032;C:411510218;G:422103800;T:517279706;N:0 944       549431032 411510218 422103800 517279706 0 ERX4273969 ERS4808635 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9924 9924 ERR4326350 ERX4273208 ERS4808398 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   430 LNA 6h rep1 430 LNA 6h rep1 SAMEA7047764 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-H8_PDBN059569.tar.gz nanopore 722817654.0 657296.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 0:1099.68 A:206996491;C:157022109;G:155085437;T:203713617;N:0 1099       206996491 157022109 155085437 203713617 0 ERX4273208 ERS4808398 ERA2764399 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9925 9925 ERR4335436 ERX4282181 ERS4818366 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep2 WT 6h rep2 JD W23 PRPN039928   ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-W23_PRPN039928.tar.gz nanopore 1268761319.0 1385621.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1 0:915.66 A:366823862;C:275507684;G:284634548;T:341795225;N:0 915       366823862 275507684 284634548 341795225 0 ERX4282181 ERS4818366 ERA2769006 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9926 9926 ERR4321680 ERX4268538 ERS4808125 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 0h rep1 WT 0h rep1 JD A1 GDDN003032   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 GridION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE GridION   ERP122761 GridION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-A1_GDDN003032.tar.gz nanopore 753417826.0 698774.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 0:1078.20 A:214525685;C:165042952;G:171160615;T:202688574;N:0 1078       214525685 165042952 171160615 202688574 0 ERX4268538 ERS4808125 ERA2763718 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
11833 11833 ERR11872224 ERX11269666 ERS16284435 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 9 SAMEA114295326 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295326|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 9|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 9|scientific name:Danio rerio|strain:AB|tank:T13                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 9 s Sample 9 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1100sR1436.fastq.gz fastq 1961832438.0 38853673.0 E MTAB 13269:Sample 9 0:50.49 A:498124499;C:481739620;G:459005215;T:520487633;N:2475471 50       498124499 481739620 459005215 520487633 2475471 ERX11269666 ERS16284435 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11834 11834 ERR11872220 ERX11269662 ERS16284431 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 5 SAMEA114295322 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295322|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 5|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 5|scientific name:Danio rerio|strain:AB|tank:T8                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 5 s Sample 5 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1137sR1431.fastq.gz fastq 1384318515.0 27436121.0 E MTAB 13269:Sample 5 0:50.46 A:351376207;C:340294254;G:322773331;T:366105473;N:3769250 50       351376207 340294254 322773331 366105473 3769250 ERX11269662 ERS16284431 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11835 11835 ERR11872216 ERX11269658 ERS16284427 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 1 SAMEA114295318 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295318|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 1|scientific name:Danio rerio|strain:AB|tank:T7                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 1 s Sample 1 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1067sR1425.fastq.gz fastq 2542543911.0 50536210.0 E MTAB 13269:Sample 1 0:50.31 A:650946248;C:611164311;G:577961102;T:679442750;N:23029500 50       650946248 611164311 577961102 679442750 23029500 ERX11269658 ERS16284427 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11836 11836 ERR11872218 ERX11269660 ERS16284429 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 3 SAMEA114295320 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295320|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 3|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 3|scientific name:Danio rerio|strain:AB|tank:T7                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 3 s Sample 3 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1100sR1428.fastq.gz fastq 1504139674.0 29976579.0 E MTAB 13269:Sample 3 0:50.18 A:378815411;C:361930389;G:348289715;T:391168927;N:23935232 50       378815411 361930389 348289715 391168927 23935232 ERX11269660 ERS16284429 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11837 11837 ERR11872219 ERX11269661 ERS16284430 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 4 SAMEA114295321 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295321|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 4|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 4|scientific name:Danio rerio|strain:AB|tank:T8                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 4 s Sample 4 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1067sR1429.fastq.gz fastq 1287164622.0 25539878.0 E MTAB 13269:Sample 4 0:50.40 A:326779989;C:313960441;G:299210114;T:340187543;N:7026535 50       326779989 313960441 299210114 340187543 7026535 ERX11269661 ERS16284430 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11838 11838 ERR11872222 ERX11269664 ERS16284433 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 7 SAMEA114295324 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295324|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 7|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 7|scientific name:Danio rerio|strain:AB|tank:T13                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 7 s Sample 7 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1067sR1433.fastq.gz fastq 2055723538.0 40748974.0 E MTAB 13269:Sample 7 0:50.45 A:530988871;C:494680653;G:471905883;T:551730327;N:6417804 50       530988871 494680653 471905883 551730327 6417804 ERX11269664 ERS16284433 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11839 11839 ERR11872221 ERX11269663 ERS16284432 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 6 SAMEA114295323 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295323|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 6|scientific name:Danio rerio|strain:AB|tank:T8                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 6 s Sample 6 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1100sR1432.fastq.gz fastq 1541862753.0 30534298.0 E MTAB 13269:Sample 6 0:50.50 A:390914024;C:378834682;G:362325696;T:407660220;N:2128131 50       390914024 378834682 362325696 407660220 2128131 ERX11269663 ERS16284432 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11840 11840 ERR11872217 ERX11269659 ERS16284428 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 2 SAMEA114295319 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295319|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 2|scientific name:Danio rerio|strain:AB|tank:T7                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 2 s Sample 2 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1067sR1427.fastq.gz fastq 1120463267.0 22442762.0 E MTAB 13269:Sample 2 0:49.93 A:283544047;C:261601041;G:250663913;T:294648349;N:30005917 49       283544047 261601041 250663913 294648349 30005917 ERX11269659 ERS16284428 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11841 11841 ERR11872223 ERX11269665 ERS16284434 ERP150458 PRJEB65329 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-13269 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 8 SAMEA114295325 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295325|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 8|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 8|scientific name:Danio rerio|strain:AB|tank:T13                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 13269:Sample 8 s Sample 8 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150458 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1067sR1435.fastq.gz fastq 2492217928.0 49578248.0 E MTAB 13269:Sample 8 0:50.27 A:633127675;C:599191649;G:572355526;T:659345988;N:28197090 50       633127675 599191649 572355526 659345988 28197090 ERX11269665 ERS16284434 ERA26965226 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11842 11842 ERR11872230 ERX11269672 ERS16284439 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 4 SAMEA114295330 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295330|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 4|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 4|scientific name:Danio rerio|strain:AB|tank:T8                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 4 s Sample 4 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s2-R1718-dre-nc-metalaxyl_Eilebrecht.fastq.gz fastq 3090739917.0 61141982.0 E MTAB 13270:Sample 4 0:50.55 A:757773770;C:707158595;G:708507725;T:915894260;N:1405567 50       757773770 707158595 708507725 915894260 1405567 ERX11269672 ERS16284439 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11843 11843 ERR11872228 ERX11269670 ERS16284437 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 2 SAMEA114295328 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295328|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 2|scientific name:Danio rerio|strain:AB|tank:T6                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 2 s Sample 2 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s1-R1716-dre-C2-metalaxyl_Eilebrecht.fastq.gz fastq 2700642168.0 53433052.0 E MTAB 13270:Sample 2 0:50.54 A:669595678;C:619368901;G:590427891;T:819827582;N:1422116 50       669595678 619368901 590427891 819827582 1422116 ERX11269670 ERS16284437 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11844 11844 ERR11872227 ERX11269669 ERS16284436 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 1 SAMEA114295327 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295327|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 1|scientific name:Danio rerio|strain:AB|tank:T6                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 1 s Sample 1 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s1-R1714-dre-nc-metalaxyl_Eilebrecht.fastq.gz fastq 2274694218.0 45004376.0 E MTAB 13270:Sample 1 0:50.54 A:562285999;C:518447937;G:499619290;T:693250049;N:1090943 50       562285999 518447937 499619290 693250049 1090943 ERX11269669 ERS16284436 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11845 11845 ERR11872231 ERX11269673 ERS16284440 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 5 SAMEA114295331 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295331|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 5|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 5|scientific name:Danio rerio|strain:AB|tank:T8                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 5 s Sample 5 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s2-R1720-dre-C2-metalaxyl_Eilebrecht.fastq.gz fastq 2777053633.0 54933357.0 E MTAB 13270:Sample 5 0:50.55 A:677084481;C:642868295;G:614554344;T:841210183;N:1336330 50       677084481 642868295 614554344 841210183 1336330 ERX11269673 ERS16284440 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11846 11846 ERR11872229 ERX11269671 ERS16284438 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 3 SAMEA114295329 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295329|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 3|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 3|scientific name:Danio rerio|strain:AB|tank:T6                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 3 s Sample 3 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s1-R1717-dre-C3-metalaxyl_Eilebrecht.fastq.gz fastq 2503234144.0 49524111.0 E MTAB 13270:Sample 3 0:50.55 A:612103203;C:572993175;G:554869755;T:761847743;N:1420268 50       612103203 572993175 554869755 761847743 1420268 ERX11269671 ERS16284438 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11847 11847 ERR11872233 ERX11269675 ERS16284442 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 7 SAMEA114295333 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295333|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 7|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 7|scientific name:Danio rerio|strain:AB|tank:T9                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 7 s Sample 7 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s3-R1722-dre-nc-metalaxyl_Eilebrecht.fastq.gz fastq 2210069991.0 43725261.0 E MTAB 13270:Sample 7 0:50.54 A:543075905;C:511224703;G:487348154;T:667396647;N:1024582 50       543075905 511224703 487348154 667396647 1024582 ERX11269675 ERS16284442 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11848 11848 ERR11872234 ERX11269676 ERS16284443 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 8 SAMEA114295334 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295334|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 8|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 8|scientific name:Danio rerio|strain:AB|tank:T9                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 8 s Sample 8 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s3-R1724-dre-C2-metalaxyl_Eilebrecht.fastq.gz fastq 2289618271.0 45294560.0 E MTAB 13270:Sample 8 0:50.55 A:560540697;C:527453035;G:507883622;T:692636061;N:1104856 50       560540697 527453035 507883622 692636061 1104856 ERX11269676 ERS16284443 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11849 11849 ERR11872235 ERX11269677 ERS16284444 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 9 SAMEA114295335 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295335|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 9|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 9|scientific name:Danio rerio|strain:AB|tank:T9                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 9 s Sample 9 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s3-R1725-dre-C3-metalaxyl_Eilebrecht.fastq.gz fastq 2164282095.0 42813111.0 E MTAB 13270:Sample 9 0:50.55 A:526798074;C:499625113;G:480175291;T:656576036;N:1107581 50       526798074 499625113 480175291 656576036 1107581 ERX11269677 ERS16284444 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
11850 11850 ERR11872232 ERX11269674 ERS16284441 ERP150460 PRJEB65331 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E-MTAB-13270 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01   Protocols: : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. Sample 6 SAMEA114295332 Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295332|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 6|scientific name:Danio rerio|strain:AB|tank:T8                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups E MTAB 13270:Sample 6 s Sample 6 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups : at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA.   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP150460 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 p1201s2-R1721-dre-C3-metalaxyl_Eilebrecht.fastq.gz fastq 2333796132.0 46171402.0 E MTAB 13270:Sample 6 0:50.55 A:571724946;C:541769310;G:513423860;T:705671180;N:1206836 50       571724946 541769310 513423860 705671180 1206836 ERX11269674 ERS16284441 ERA26965713 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2024-01-01 Undetermined Embryo Whole Organism All anatomical structures
19140 19140 ERR13769875 ERX13170676 ERS21156063 ERP165027 PRJEB81172 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-14536 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 1 SAMEA116134556 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA first public:2025 04 30|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC status:public|Submitter Id:E MTAB 14536:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14536:Sample 1|scientific name:Danio rerio|strain:AB|tank:T7                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 14536:Sample 1 s Sample 1 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP165027 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30 p1067sR1426.fastq.gz fastq 1044742413.0 20762139.0 E MTAB 14536:Sample 1 0:50.32 A:250471042;C:265283643;G:251710894;T:266877610;N:10399224 50       250471042 265283643 251710894 266877610 10399224 ERX13170676 ERS21156063 ERA30873015 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2025-04-30 Undetermined Embryo Whole Organism All anatomical structures
19141 19141 ERR13769876 ERX13170677 ERS21156064 ERP165027 PRJEB81172 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-14536 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 2 SAMEA116134557 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA first public:2025 04 30|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC status:public|Submitter Id:E MTAB 14536:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14536:Sample 2|scientific name:Danio rerio|strain:AB|tank:T8                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 14536:Sample 2 s Sample 2 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP165027 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30 p1067sR1430.fastq.gz fastq 1360497810.0 27516448.0 E MTAB 14536:Sample 2 0:49.44 A:337559200;C:309495128;G:294605904;T:352033780;N:66803798 49       337559200 309495128 294605904 352033780 66803798 ERX13170677 ERS21156064 ERA30873015 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2025-04-30 Undetermined Embryo Whole Organism All anatomical structures
19142 19142 ERR13769877 ERX13170678 ERS21156065 ERP165027 PRJEB81172 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E-MTAB-14536 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30   Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA Sample 3 SAMEA116134558 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA first public:2025 04 30|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC status:public|Submitter Id:E MTAB 14536:Sample 3|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14536:Sample 3|scientific name:Danio rerio|strain:AB|tank:T13                 mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups E MTAB 14536:Sample 3 s Sample 3 s mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP165027 Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30 p1067sR1434.fastq.gz fastq 1537549016.0 31165038.0 E MTAB 14536:Sample 3 0:49.34 A:379537732;C:349448626;G:332769302;T:392738674;N:83054682 49       379537732 349448626 332769302 392738674 83054682 ERX13170678 ERS21156065 ERA30873015 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2025-04-30 Undetermined Embryo Whole Organism All anatomical structures
25320 25320 SRR25810878 SRX21533024 SRS18745490 SRP457576 PRJNA1010780 Effect of egr3 knockout on gene expression of dissected zebrafish hearts GSE241935 Transcriptome Analysis To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571   pubmed:38748804   egr3 wild type siblings 2 GSM7745909   source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing egr3 wild type siblings 2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts Heart   Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.   tissue:Heart|genotype:bns577+/+ GSM7745909 GSM7745909: egr3 wild type siblings 2; Danio rerio; RNA Seq GSM7745909 r1 GSM7745909 1 Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP457576   loader:fastq load.py E22_3626_Lib_Agatha_egr3_WT2_R1.fastq.gz fastq 3473319384.0 49279465.0 GSM7745909 r1 0:70.48 A:943794847;C:792135324;G:792042625;T:945083925;N:262663 70       943794847 792135324 792042625 945083925 262663 SRX21533024 SRS18745490 SRA1702458 MPI for heart and lung research MPI for heart and lung research 1 0.68549   0.04588   0.76865   0.44964   71   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2023-08-30 Undetermined Undetermined Heart Cardiovascular System
25321 25321 SRR25810879 SRX21533023 SRS18745489 SRP457576 PRJNA1010780 Effect of egr3 knockout on gene expression of dissected zebrafish hearts GSE241935 Transcriptome Analysis To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571   pubmed:38748804   egr3 wild type siblings 1 GSM7745908   source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing egr3 wild type siblings 1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts Heart   Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.   tissue:Heart|genotype:bns577+/+ GSM7745908 GSM7745908: egr3 wild type siblings 1; Danio rerio; RNA Seq GSM7745908 r1 GSM7745908 1 Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP457576   loader:fastq load.py E22_3626_Lib_Agatha_egr3_WT1_R1.fastq.gz fastq 3909248616.0 55045571.0 GSM7745908 r1 0:71.02 A:1048107387;C:905014546;G:907455489;T:1048528690;N:142504 71       1048107387 905014546 907455489 1048528690 142504 SRX21533023 SRS18745489 SRA1702458 MPI for heart and lung research MPI for heart and lung research 1 0.94958   0.06298   0.74819   0.45762   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2023-08-30 Undetermined Undetermined Heart Cardiovascular System
25322 25322 SRR25810880 SRX21533022 SRS18745488 SRP457576 PRJNA1010780 Effect of egr3 knockout on gene expression of dissected zebrafish hearts GSE241935 Transcriptome Analysis To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571   pubmed:38748804   egr3 mutants 2 GSM7745907   source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing egr3 mutants 2 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts Heart   Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.   tissue:Heart|genotype:bns577 / GSM7745907 GSM7745907: egr3 mutants 2; Danio rerio; RNA Seq GSM7745907 r1 GSM7745907 1 Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP457576   loader:fastq load.py E22_3626_Lib_Agatha_egr3_Mut2_R1.fastq.gz fastq 3432675258.0 48483287.0 GSM7745907 r1 0:70.80 A:925832958;C:788551205;G:790129536;T:927993012;N:168547 70       925832958 788551205 790129536 927993012 168547 SRX21533022 SRS18745488 SRA1702458 MPI for heart and lung research MPI for heart and lung research 1 0.75652   0.04046   0.76455   0.46333   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2023-08-30 Undetermined Undetermined Heart Cardiovascular System
25323 25323 SRR25810881 SRX21533021 SRS18745487 SRP457576 PRJNA1010780 Effect of egr3 knockout on gene expression of dissected zebrafish hearts GSE241935 Transcriptome Analysis To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571   pubmed:38748804   egr3 mutants 1 GSM7745906   source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing egr3 mutants 1 Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts Heart   Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.   tissue:Heart|genotype:bns577 / GSM7745906 GSM7745906: egr3 mutants 1; Danio rerio; RNA Seq GSM7745906 r1 GSM7745906 1 Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 2000   SRP457576   loader:fastq load.py E22_3626_Lib_Agatha_egr3_Mut1_R1.fastq.gz fastq 3838969347.0 54545950.0 GSM7745906 r1 0:70.38 A:1016913415;C:902500250;G:903033204;T:1016194618;N:327860 70       1016913415 902500250 903033204 1016194618 327860 SRX21533021 SRS18745487 SRA1702458 MPI for heart and lung research MPI for heart and lung research 1 0.9511   0.05017   0.75341   0.47152   72   B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2023-08-30 Undetermined Undetermined Heart Cardiovascular System
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

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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");;