{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"cDNA\" and tissue_curation = \"Whole Organism\"", "rows": [[3016, "ERR1396840", "ERX1468099", "ERS1051447", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph230 dgcr8 B12", "SAMEA3864313", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864313|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. 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Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 2#6", "15616929", "Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. 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Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 2#5", "15616917", "Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. 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Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#20", "15616907", "Illumina sequencing of library 15616907 constructed from sample accession ERS1051444 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. 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Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#6", "15616929", "Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. 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Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#5", "15616917", "Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. 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Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#2", "15616881", "Illumina sequencing of library 15616881 constructed from sample accession ERS1051426 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CGATGT.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#2.cram", "cram", 326025150.0, 6520503.0, "SC RUN 18732 1#2", "0:50", "A:93261648;C:82767834;G:86798075;T:63166259;N:31334", 50, null, null, null, 93261648, 82767834, 86798075, 63166259, 31334, "ERX1468054", "ERS1051426", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.57333, null, 0.11365, null, 0.87422, null, 0.60838, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3062, "ERR1396794", "ERX1468053", "ERS1051425", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha B1", "SAMEA3864291", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864291|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:20Z|INSDC status:public|Submitter Id:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#1", "15616869", "Illumina sequencing of library 15616869 constructed from sample accession ERS1051425 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATCACG.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#1.cram", "cram", 419669000.0, 8393380.0, "SC RUN 18732 1#1", "0:50", "A:121378853;C:106010609;G:109826454;T:82412717;N:40367", 50, null, null, null, 121378853, 106010609, 109826454, 82412717, 40367, "ERX1468053", "ERS1051425", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.60815, null, 0.11567, null, 0.90289, null, 0.5657, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [9764, "ERR3454281", "ERX3476201", "ERS360451", "ERP116513", "PRJEB33700", "Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila", "ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961", "Other", "Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, null, "SAMEA2224102", "SC", "ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:47:37Z|External Id:SAMEA2224102|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:47:37Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 4. A 5 base indexing sequence CAAGA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409|scientific name:Danio rerio|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP116513", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, 659815100.0, 13196302.0, "ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 6", "0:50", "A:163494131;C:142490716;G:153472608;T:200319869;N:37776", 50, null, null, null, 163494131, 142490716, 153472608, 200319869, 37776, "ERX3476201", "ERS360451", "ERA2051096", "CIRI-Inserm-U1111|European Nucleotide Archive", "CIRI-Inserm-U1111", 1, 0.00278, null, 0.00206, null, 0.99922, null, 0.24031, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-03-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [9765, "ERR3454280", "ERX3476200", "ERS360450", "ERP116513", "PRJEB33700", "Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila", "ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961", "Other", "Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, null, "SAMEA2224101", "SC", "ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224101|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype32 clutch 4. A 5 base indexing sequence CGCAA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|scientific name:Danio rerio|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP116513", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, 1031629900.0, 20632598.0, "ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 5", "0:50", "A:266496533;C:234318648;G:214719546;T:316013013;N:82160", 50, null, null, null, 266496533, 234318648, 214719546, 316013013, 82160, "ERX3476200", "ERS360450", "ERA2051096", "CIRI-Inserm-U1111|European Nucleotide Archive", "CIRI-Inserm-U1111", 1, 0.003, null, 0.00187, null, 0.99902, null, 0.27272, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-03-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [9766, "ERR3454279", "ERX3476199", "ERS360449", "ERP116513", "PRJEB33700", "Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila", "ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961", "Other", "Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, null, "SAMEA2224100", "SC", "ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:49:06Z|External Id:SAMEA2224100|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:49:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence GCACG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407|scientific name:Danio rerio|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP116513", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, 547730200.0, 10954604.0, "ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 4", "0:50", "A:142048050;C:118592881;G:112867934;T:174179317;N:42018", 50, null, null, null, 142048050, 118592881, 112867934, 174179317, 42018, "ERX3476199", "ERS360449", "ERA2051096", "CIRI-Inserm-U1111|European Nucleotide Archive", "CIRI-Inserm-U1111", 1, 0.00355, null, 0.00226, null, 0.99902, null, 0.30487, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-03-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [9767, "ERR3454278", "ERX3476198", "ERS360448", "ERP116513", "PRJEB33700", "Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila", "ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961", "Other", "Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, null, "SAMEA2224099", "SC", "ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:47:37Z|External Id:SAMEA2224099|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:47:37Z|INSDC status:public|Submitter Id:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence CAGAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406|scientific name:Danio rerio|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP116513", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, 844323050.0, 16886461.0, "ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 3", "0:50", "A:219263127;C:181661743;G:173433057;T:269898556;N:66567", 50, null, null, null, 219263127, 181661743, 173433057, 269898556, 66567, "ERX3476198", "ERS360448", "ERA2051096", "CIRI-Inserm-U1111|European Nucleotide Archive", "CIRI-Inserm-U1111", 1, 0.00523, null, 0.00319, null, 0.99892, null, 0.2637, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-03-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [9768, "ERR3454277", "ERX3476197", "ERS360447", "ERP116513", "PRJEB33700", "Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila", "ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961", "Other", "Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, null, "SAMEA2224098", "SC", "ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224098|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence AGAAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405|scientific name:Danio rerio|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP116513", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, 600000000.0, 12000000.0, "ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 2", "0:50", "A:153130383;C:136248892;G:127363796;T:183213089;N:43840", 50, null, null, null, 153130383, 136248892, 127363796, 183213089, 43840, "ERX3476197", "ERS360447", "ERA2051096", "CIRI-Inserm-U1111|European Nucleotide Archive", "CIRI-Inserm-U1111", 1, 0.00372, null, 0.00211, null, 0.99888, null, 0.31649, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-03-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [9769, "ERR3454276", "ERX3476196", "ERS360446", "ERP116513", "PRJEB33700", "Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila", "ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961", "Other", "Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, null, "SAMEA2224097", "SC", "ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:49:06Z|External Id:SAMEA2224097|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:49:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence GAGGC is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404|scientific name:Danio rerio|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP116513", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26", null, null, 600000000.0, 12000000.0, "ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 1", "0:50", "A:153852410;C:135392627;G:125428239;T:185280608;N:46116", 50, null, null, null, 153852410, 135392627, 125428239, 185280608, 46116, "ERX3476196", "ERS360446", "ERA2051096", "CIRI-Inserm-U1111|European Nucleotide Archive", "CIRI-Inserm-U1111", 1, 0.00545, null, 0.00291, null, 0.9988, null, 0.31681, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-03-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10649, "ERR406885", "ERX373262", "ERS391761", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5s24", "SAMEA2299303", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299303|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.4", "batchA 24hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5s24.fq.gz", "fastq", 584550600.0, 11691012.0, "E MTAB 2194:5s24.fq.gz", "0:50 1:0", "A:154602150;C:138134763;G:138628704;T:153175234;N:9749", 50, 0, null, null, 154602150, 138134763, 138628704, 153175234, 9749, "ERX373262", "ERS391761", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.9356, null, 0.0996, null, 0.68615, null, 0.47069, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10650, "ERR406893", "ERX373261", "ERS391760", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5y32", "SAMEA2299302", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299302|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.5", "batchA 32hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5y32.fq.gz", "fastq", 528892950.0, 10577859.0, "E MTAB 2194:5y32.fq.gz", "0:50 1:0", "A:140383478;C:125036983;G:124119152;T:139344643;N:8694", 50, 0, null, null, 140383478, 125036983, 124119152, 139344643, 8694, "ERX373261", "ERS391760", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93478, null, 0.10542, null, 0.68296, null, 0.4795, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10651, "ERR406898", "ERX373260", "ERS391759", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6s24", "SAMEA2299301", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299301|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.10", "batchB 24hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6s24.fq.gz", "fastq", 542771850.0, 10855437.0, "E MTAB 2194:6s24.fq.gz", "0:50 1:0", "A:142311943;C:129686202;G:129130172;T:141634727;N:8806", 50, 0, null, null, 142311943, 129686202, 129130172, 141634727, 8806, "ERX373260", "ERS391759", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93717, null, 0.09239, null, 0.68876, null, 0.46809, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10652, "ERR406896", "ERX373259", "ERS391758", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13y32", "SAMEA2299300", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299300|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.18", "batchC 32hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13y32.fq.gz", "fastq", 649898350.0, 12997967.0, "E MTAB 2194:13y32.fq.gz", "0:50 1:0", "A:169738689;C:156130165;G:155102788;T:168916174;N:10534", 50, 0, null, null, 169738689, 156130165, 155102788, 168916174, 10534, "ERX373259", "ERS391758", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93898, null, 0.08535, null, 0.68217, null, 0.47133, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10653, "ERR406899", "ERX373258", "ERS391757", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5s32", "SAMEA2299299", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299299|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.6", "batchA 32hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5s32.fq.gz", "fastq", 566813600.0, 11336272.0, "E MTAB 2194:5s32.fq.gz", "0:50 1:0", "A:149907366;C:134421172;G:133399280;T:149076590;N:9192", 50, 0, null, null, 149907366, 134421172, 133399280, 149076590, 9192, "ERX373258", "ERS391757", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93497, null, 0.10019, null, 0.68379, null, 0.4671, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10654, "ERR406888", "ERX373257", "ERS391756", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5y24", "SAMEA2299298", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299298|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.3", "batchA 24hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5y24.fq.gz", "fastq", 578936250.0, 11578725.0, "E MTAB 2194:5y24.fq.gz", "0:50 1:0", "A:154884020;C:135497257;G:135214353;T:153331273;N:9347", 50, 0, null, null, 154884020, 135497257, 135214353, 153331273, 9347, "ERX373257", "ERS391756", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.9342, null, 0.1106, null, 0.67811, null, 0.47685, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10655, "ERR406887", "ERX373256", "ERS391755", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13s24", "SAMEA2299297", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299297|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.16", "batchC 24hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13s24.fq.gz", "fastq", 837415050.0, 16748301.0, "E MTAB 2194:13s24.fq.gz", "0:50 1:0", "A:217172462;C:202556518;G:201365353;T:216307386;N:13331", 50, 0, null, null, 217172462, 202556518, 201365353, 216307386, 13331, "ERX373256", "ERS391755", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93888, null, 0.07561, null, 0.6899, null, 0.46646, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10656, "ERR406894", "ERX373255", "ERS391754", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6y24", "SAMEA2299296", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299296|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.9", "batchB 24hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6y24.fq.gz", "fastq", 569424550.0, 11388491.0, "E MTAB 2194:6y24.fq.gz", "0:50 1:0", "A:149287318;C:136121879;G:135445765;T:148560272;N:9316", 50, 0, null, null, 149287318, 136121879, 135445765, 148560272, 9316, "ERX373255", "ERS391754", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93486, null, 0.0893, null, 0.68751, null, 0.46133, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10657, "ERR406895", "ERX373254", "ERS391753", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13s8", "SAMEA2299295", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299295|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.14", "batchC 8hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13s8.fq.gz", "fastq", 532141500.0, 10642830.0, "E MTAB 2194:13s8.fq.gz", "0:50 1:0", "A:139773245;C:127051350;G:126773752;T:138534560;N:8593", 50, 0, null, null, 139773245, 127051350, 126773752, 138534560, 8593, "ERX373254", "ERS391753", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93506, null, 0.0742, null, 0.74748, null, 0.47765, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10658, "ERR406891", "ERX373253", "ERS391752", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6s8", "SAMEA2299294", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299294|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.8", "batchB 8hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6s8.fq.gz", "fastq", 477620550.0, 9552411.0, "E MTAB 2194:6s8.fq.gz", "0:50 1:0", "A:127095393;C:112660046;G:111717464;T:126139686;N:7961", 50, 0, null, null, 127095393, 112660046, 111717464, 126139686, 7961, "ERX373253", "ERS391752", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93605, null, 0.08112, null, 0.74552, null, 0.46821, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10659, "ERR406886", "ERX373252", "ERS391751", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6y8", "SAMEA2299293", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299293|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.7", "batchB 8hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6y8.fq.gz", "fastq", 508637450.0, 10172749.0, "E MTAB 2194:6y8.fq.gz", "0:50 1:0", "A:135377293;C:119833844;G:119447157;T:133970958;N:8198", 50, 0, null, null, 135377293, 119833844, 119447157, 133970958, 8198, "ERX373252", "ERS391751", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93203, null, 0.07833, null, 0.73744, null, 0.47586, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10660, "ERR406892", "ERX373251", "ERS391750", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6y32", "SAMEA2299292", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299292|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:6y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.11", "batchB 32hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6y32.fq.gz", "fastq", 568482400.0, 11369648.0, "E MTAB 2194:6y32.fq.gz", "0:50 1:0", "A:149679881;C:135411801;G:134312216;T:149069222;N:9280", 50, 0, null, null, 149679881, 135411801, 134312216, 149069222, 9280, "ERX373251", "ERS391750", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93184, null, 0.104, null, 0.68128, null, 0.47652, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10661, "ERR406897", "ERX373250", "ERS391749", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5y8", "SAMEA2299291", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299291|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:5y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.1", "batchA 8hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5y8.fq.gz", "fastq", 497573200.0, 9951464.0, "E MTAB 2194:5y8.fq.gz", "0:50 1:0", "A:134128000;C:115688460;G:114668036;T:133080206;N:8498", 50, 0, null, null, 134128000, 115688460, 114668036, 133080206, 8498, "ERX373250", "ERS391749", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93519, null, 0.07057, null, 0.73511, null, 0.47977, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10662, "ERR406889", "ERX373249", "ERS391748", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13s32", "SAMEA2299290", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299290|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:13s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.19", "batchC 32hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13s32.fq.gz", "fastq", 637724150.0, 12754483.0, "E MTAB 2194:13s32.fq.gz", "0:50 1:0", "A:165500205;C:154383334;G:152953181;T:164877160;N:10270", 50, 0, null, null, 165500205, 154383334, 152953181, 164877160, 10270, "ERX373249", "ERS391748", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93998, null, 0.08954, null, 0.68146, null, 0.4729, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10663, "ERR406890", "ERX373248", "ERS391747", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13y24", "SAMEA2299289", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299289|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:13y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.15", "batchC 24hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13y24.fq.gz", "fastq", 834725800.0, 16694516.0, "E MTAB 2194:13y24.fq.gz", "0:50 1:0", "A:216896952;C:201332171;G:200308143;T:216174965;N:13569", 50, 0, null, null, 216896952, 201332171, 200308143, 216174965, 13569, "ERX373248", "ERS391747", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.9358, null, 0.07569, null, 0.68757, null, 0.46994, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10664, "ERR406900", "ERX373247", "ERS391746", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13y8", "SAMEA2299288", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299288|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:13y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.13", "batchC 8hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13y8.fq.gz", "fastq", 457245150.0, 9144903.0, "E MTAB 2194:13y8.fq.gz", "0:50 1:0", "A:119648940;C:109589521;G:109491446;T:118507707;N:7536", 50, 0, null, null, 119648940, 109589521, 109491446, 118507707, 7536, "ERX373247", "ERS391746", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93146, null, 0.0681, null, 0.73718, null, 0.47464, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10665, "ERR406884", "ERX373246", "ERS391745", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6s32", "SAMEA2299287", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299287|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:6s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.12", "batchB 32hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6s32.fq.gz", "fastq", 652353200.0, 13047064.0, "E MTAB 2194:6s32.fq.gz", "0:50 1:0", "A:170844587;C:156203331;G:155264927;T:170029850;N:10505", 50, 0, null, null, 170844587, 156203331, 155264927, 170029850, 10505, "ERX373246", "ERS391745", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93785, null, 0.09102, null, 0.68554, null, 0.46397, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10666, "ERR406901", "ERX373245", "ERS391744", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability we partially remove the yolk during embryogenesis. Around 5 hpf we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8 24 hpf and 32 hpf we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5s8", "SAMEA2299286", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299286|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:5s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.2", "batchA 8hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5s8.fq.gz", "fastq", 359298500.0, 7185970.0, "E MTAB 2194:5s8.fq.gz", "0:50 1:0", "A:96450828;C:83805020;G:83440885;T:95595844;N:5923", 50, 0, null, null, 96450828, 83805020, 83440885, 95595844, 5923, "ERX373245", "ERS391744", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93524, null, 0.07491, null, 0.73312, null, 0.47914, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [25273, "SRR25764091", "SRX21486763", "SRS18719063", "SRP457108", "PRJNA1009807", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]", "GSE241752", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT bud 10 hpf RNA seq rep2", "GSM7734768", null, "source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT bud 10 hpf RNA seq rep2", "3\u2019 adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length \u226520. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation", "Gastrula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT", "GSM7734768", "GSM7734768: WT bud 10 hpf RNA seq rep2; Danio rerio; RNA Seq", "GSM7734768 r1", "GSM7734768", "1", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457108", null, null, "WT_mRNA_bud_2.fastq.gz", "fastq", 2470912004.0, 31168086.0, "GSM7734768 r1", "0:79.28", "A:656817108;C:568241258;G:504262095;T:741507737;N:83806", 79, null, null, null, 656817108, 568241258, 504262095, 741507737, 83806, "SRX21486763", "SRS18719063", "SRA1700431", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.91479, null, 0.27298, null, 0.74231, null, 0.57302, null, 79, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2023-08-28", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [25274, "SRR25764092", "SRX21486762", "SRS18719064", "SRP457108", "PRJNA1009807", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]", "GSE241752", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT bud 10 hpf RNA seq rep1", "GSM7734767", null, "source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT bud 10 hpf RNA seq rep1", "3\u2019 adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length \u226520. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation", "Gastrula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT", "GSM7734767", "GSM7734767: WT bud 10 hpf RNA seq rep1; Danio rerio; RNA Seq", "GSM7734767 r1", "GSM7734767", "1", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457108", null, null, "WT_mRNA_bud_1.fastq.gz", "fastq", 2153494756.0, 27140032.0, "GSM7734767 r1", "0:79.35", "A:560793143;C:508962676;G:445126772;T:638539310;N:72855", 79, null, null, null, 560793143, 508962676, 445126772, 638539310, 72855, "SRX21486762", "SRS18719064", "SRA1700431", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.88728, null, 0.25493, null, 0.74369, null, 0.56589, null, 80, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2023-08-28", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [25275, "SRR25764093", "SRX21486761", "SRS18719061", "SRP457108", "PRJNA1009807", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]", "GSE241752", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf RNA seq rep2", "GSM7734766", null, "source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT sphere 4 hpf RNA seq rep2", "3\u2019 adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length \u226520. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation", "Blastula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT", "GSM7734766", "GSM7734766: WT sphere 4 hpf RNA seq rep2; Danio rerio; RNA Seq", "GSM7734766 r1", "GSM7734766", "1", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457108", null, null, "WT_mRNA_sphere_2.fastq.gz", "fastq", 2455317157.0, 30934591.0, "GSM7734766 r1", "0:79.37", "A:614860604;C:588586084;G:522132289;T:729655621;N:82559", 79, null, null, null, 614860604, 588586084, 522132289, 729655621, 82559, "SRX21486761", "SRS18719061", "SRA1700431", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.94124, null, 0.10502, null, 0.74876, null, 0.57752, null, 80, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2023-08-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [25276, "SRR25764094", "SRX21486760", "SRS18719060", "SRP457108", "PRJNA1009807", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq]", "GSE241752", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf RNA seq rep1", "GSM7734765", null, "source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT sphere 4 hpf RNA seq rep1", "3\u2019 adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length \u226520. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation", "Blastula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT", "GSM7734765", "GSM7734765: WT sphere 4 hpf RNA seq rep1; Danio rerio; RNA Seq", "GSM7734765 r1", "GSM7734765", "1", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457108", null, null, "WT_mRNA_sphere_1.fastq.gz", "fastq", 2399640874.0, 30232118.0, "GSM7734765 r1", "0:79.37", "A:589069860;C:593745131;G:511439690;T:705305674;N:80519", 79, null, null, null, 589069860, 593745131, 511439690, 705305674, 80519, "SRX21486760", "SRS18719060", "SRA1700431", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.85882, null, 0.11848, null, 0.75122, null, 0.5883, null, 80, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2023-08-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [28113, "SRR26209648", "SRX21920662", "SRS19005181", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 3", "GSM7812991", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 152808626, 149738763, 141639387, 172257280, 5303, "SRX21920662", "SRS19005181", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94246, null, 0.08766, null, 0.69443, null, 0.4842, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28114, "SRR26209649", "SRX21920662", "SRS19005181", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 3", "GSM7812991", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 151226657, 148143193, 140088806, 170530812, 9829, "SRX21920662", "SRS19005181", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94201, null, 0.08569, null, 0.69572, null, 0.48692, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28115, "SRR26209650", "SRX21920662", "SRS19005181", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 3", "GSM7812991", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 134685766, 132190291, 124881864, 151967639, 4910, "SRX21920662", "SRS19005181", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.9431, null, 0.08733, null, 0.69524, null, 0.48528, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28116, "SRR26209651", "SRX21920662", "SRS19005181", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 3", "GSM7812991", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 160756303, 158145998, 149623680, 180816390, 11778, "SRX21920662", "SRS19005181", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94438, null, 0.08618, null, 0.69473, null, 0.48809, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28117, "SRR26209752", "SRX21920662", "SRS19005181", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 3", "GSM7812991", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 161054597, 158340761, 149784923, 181251361, 18862, "SRX21920662", "SRS19005181", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94338, null, 0.08713, null, 0.6968, null, 0.48443, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28118, "SRR26209652", "SRX21920661", "SRS19005180", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 2", "GSM7812990", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 147906639, 143944406, 137307101, 163904929, 5087, "SRX21920661", "SRS19005180", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94371, null, 0.06473, null, 0.69378, null, 0.47765, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28119, "SRR26209653", "SRX21920661", "SRS19005180", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 2", "GSM7812990", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 146630863, 142829925, 136124185, 162728186, 9922, "SRX21920661", "SRS19005180", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94282, null, 0.06357, null, 0.69418, null, 0.47665, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28120, "SRR26209654", "SRX21920661", "SRS19005180", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 2", "GSM7812990", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 129905878, 126622019, 120526207, 144206853, 4790, "SRX21920661", "SRS19005180", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94508, null, 0.06499, null, 0.69367, null, 0.4834, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28121, "SRR26209655", "SRX21920661", "SRS19005180", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 2", "GSM7812990", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 155642981, 151651242, 144681951, 171847192, 11214, "SRX21920661", "SRS19005180", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94531, null, 0.06514, null, 0.69225, null, 0.48187, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28122, "SRR26209656", "SRX21920661", "SRS19005180", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 2", "GSM7812990", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 155145221, 151231599, 144290581, 171470641, 17918, "SRX21920661", "SRS19005180", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94319, null, 0.06413, null, 0.69449, null, 0.48159, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28123, "SRR26209657", "SRX21920660", "SRS19005179", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 1", "GSM7812989", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 149619230, 146559346, 139674646, 166662143, 5185, "SRX21920660", "SRS19005179", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94449, null, 0.06296, null, 0.69487, null, 0.48, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28124, "SRR26209658", "SRX21920660", "SRS19005179", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 1", "GSM7812989", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 148193962, 145221539, 138267073, 165249833, 10115, "SRX21920660", "SRS19005179", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.9446, null, 0.06327, null, 0.69562, null, 0.48183, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28125, "SRR26209659", "SRX21920660", "SRS19005179", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 1", "GSM7812989", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 132217323, 129660296, 123303893, 147352732, 4820, "SRX21920660", "SRS19005179", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94579, null, 0.06237, null, 0.69554, null, 0.46658, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28126, "SRR26209660", "SRX21920660", "SRS19005179", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 1", "GSM7812989", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 157286526, 154336036, 147137950, 174565295, 11762, "SRX21920660", "SRS19005179", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94562, null, 0.06294, null, 0.69489, null, 0.47406, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28127, "SRR26209661", "SRX21920660", "SRS19005179", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 WT 1", "GSM7812989", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 157845668, 154972063, 147765532, 175449801, 18476, "SRX21920660", "SRS19005179", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.9471, null, 0.06288, null, 0.69536, null, 0.4797, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28128, "SRR26209662", "SRX21920659", "SRS19005178", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 3", "GSM7812988", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 173104307, 161481671, 152542615, 187053812, 6230, "SRX21920659", "SRS19005178", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94039, null, 0.07795, null, 0.69877, null, 0.48386, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28129, "SRR26209663", "SRX21920659", "SRS19005178", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 3", "GSM7812988", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 171316049, 159786547, 150743446, 185190228, 12069, "SRX21920659", "SRS19005178", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94064, null, 0.07881, null, 0.69767, null, 0.48162, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28130, "SRR26209664", "SRX21920659", "SRS19005178", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 3", "GSM7812988", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 153131508, 143126741, 134745614, 165635953, 5867, "SRX21920659", "SRS19005178", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94156, null, 0.07795, null, 0.69751, null, 0.4833, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28131, "SRR26209665", "SRX21920659", "SRS19005178", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 3", "GSM7812988", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 183100436, 171026605, 161510527, 196734608, 13750, "SRX21920659", "SRS19005178", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94298, null, 0.07892, null, 0.6997, null, 0.48331, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28132, "SRR26209666", "SRX21920659", "SRS19005178", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 3", "GSM7812988", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 183454698, 171554090, 162064705, 197567065, 20797, "SRX21920659", "SRS19005178", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94316, null, 0.07877, null, 0.70051, null, 0.48354, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28133, "SRR26209667", "SRX21920658", "SRS19005177", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 2", "GSM7812987", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 154668392, 147817141, 139653400, 169756342, 5448, "SRX21920658", "SRS19005177", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94636, null, 0.08022, null, 0.69962, null, 0.48201, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28134, "SRR26209668", "SRX21920658", "SRS19005177", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 2", "GSM7812987", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 152346877, 145640105, 137576284, 167398281, 10271, "SRX21920658", "SRS19005177", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94549, null, 0.08086, null, 0.69781, null, 0.47842, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28135, "SRR26209669", "SRX21920658", "SRS19005177", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 2", "GSM7812987", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 136317506, 130390122, 122927887, 149606028, 5032, "SRX21920658", "SRS19005177", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94653, null, 0.08075, null, 0.69704, null, 0.48374, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28136, "SRR26209670", "SRX21920658", "SRS19005177", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 2", "GSM7812987", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 162743675, 155711536, 147135700, 177594459, 12223, "SRX21920658", "SRS19005177", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94757, null, 0.08023, null, 0.70055, null, 0.48458, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28137, "SRR26209671", "SRX21920658", "SRS19005177", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 2", "GSM7812987", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 162915651, 155935181, 147406641, 178079118, 19472, "SRX21920658", "SRS19005177", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94817, null, 0.08218, null, 0.70017, null, 0.48286, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28138, "SRR26209672", "SRX21920657", "SRS19005176", "SRP463749", "PRJNA1022096", "Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses", "GSE244291", "Transcriptome Analysis", "The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament t1 and t2. Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA seq to to identify any differences in the DNA damage response between WT and fam83fa / mutants. Treatments: AD = Actinomycin D in DMSO vehicle IR = ionizing radiation 20 Grays gamma radiation unDMSO = untreated AD control vehicle only i.e. DMSO un = untreated IR control", null, "pubmed:39437839", null, "unDMSO t1 K2 1", "GSM7812986", null, "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 \u22dc 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP463749", null, "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, null, null, null, 156934542, 147417998, 139301915, 172336421, 5498, "SRX21920657", "SRS19005176", "SRA1722794", "Devenport, Molecular Biology, Princeton University", "Devenport, Molecular Biology, Princeton University", 1, 0.94179, null, 0.07628, null, 0.69512, null, 0.48041, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-09-28", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 4207, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "cDNA", "p2": "Whole Organism"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Whole+Organism", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 4183, 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