{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\" and tissue_curation = \"Undetermined\"", "rows": [[0, "DRR314108", "DRX303511", "DRS233566", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of wild type sibling sample3", "SAMD00399013", null, "sample name:rna rw337 48hpf WT rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399013", "DRX303511", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399013", null, null, null, 23076492885.0, 76679376.0, "DRR314108", "0:150.51 1:150.44", "A:6146969533;C:5373690527;G:5458576301;T:6095818756;N:1437768", 150, 150, null, null, 6146969533, 5373690527, 5458576301, 6095818756, 1437768, "DRX303511", "DRS233566", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.94223, 0.94614, 0.10721, 0.10288, 0.68745, 0.68621, 0.4728, 0.47157, 151, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [1, "DRR314107", "DRX303510", "DRS233565", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. 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All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of banp mutant sample3", "SAMD00399010", null, "sample name:rna rw337 48hpf Mutant rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399010", "DRX303508", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399010", null, null, null, 27688386114.0, 92009317.0, "DRR314105", "0:150.49 1:150.44", "A:7681451080;C:6071566134;G:6242782106;T:7690830655;N:1756139", 150, 150, null, null, 7681451080, 6071566134, 6242782106, 7690830655, 1756139, "DRX303508", "DRS233563", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.91038, 0.91556, 0.17971, 0.16967, 0.67718, 0.67716, 0.47042, 0.46425, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [4, "DRR314104", "DRX303507", "DRS233562", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of banp mutant sample2", "SAMD00399009", null, "sample name:rna rw337 48hpf Mutant rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399009", "DRX303507", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399009", null, null, null, 22970994572.0, 76322352.0, "DRR314104", "0:150.52 1:150.46", "A:6142535654;C:5310453740;G:5430124468;T:6086516676;N:1364034", 150, 150, null, null, 6142535654, 5310453740, 5430124468, 6086516676, 1364034, "DRX303507", "DRS233562", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.93707, 0.94063, 0.12175, 0.11613, 0.67825, 0.67649, 0.46485, 0.46905, 147, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [5, "DRR314103", "DRX303506", "DRS233561", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of banp mutant sample1", "SAMD00399008", null, "sample name:rna rw337 48hpf Mutant rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399008", "DRX303506", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399008", null, null, null, 23637901630.0, 78541449.0, "DRR314103", "0:150.51 1:150.45", "A:6359178134;C:5420730443;G:5530700546;T:6325864263;N:1428244", 150, 150, null, null, 6359178134, 5420730443, 5530700546, 6325864263, 1428244, "DRX303506", "DRS233561", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.9308, 0.93545, 0.13172, 0.12462, 0.68219, 0.6814, 0.46842, 0.46984, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [6, "DRR315802", "DRX305194", "DRS231989", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample4", "SAMD00400823", null, "sample name:rw147 2.5dpf wildtype rep 4|biological replicate:4", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400823", "DRX305194", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400823", null, null, null, 10262353995.0, 34151547.0, "DRR315802", "0:150.27 1:150.22", "A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550", 150, 150, null, null, 2735078560, 2386126821, 2433638250, 2707202814, 307550, "DRX305194", "DRS231989", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95231, 0.95295, 0.09229, 0.08773, 0.71819, 0.72107, 0.46746, 0.46617, 151, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [7, "DRR315801", "DRX305193", "DRS231988", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample3", "SAMD00400822", null, "sample name:rw147 2.5dpf wildtype rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400822", "DRX305193", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400822", null, null, null, 11516368634.0, 38355888.0, "DRR315801", "0:150.15 1:150.10", "A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954", 150, 150, null, null, 3080341643, 2678048339, 2713051368, 3044449330, 477954, "DRX305193", "DRS231988", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95353, 0.95634, 0.08909, 0.08533, 0.71374, 0.71252, 0.45986, 0.46059, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [8, "DRR315800", "DRX305192", "DRS231987", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample2", "SAMD00400821", null, "sample name:rw147 2.5dpf wildtype rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400821", "DRX305192", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400821", null, null, null, 8814057148.0, 29367513.0, "DRR315800", "0:150.09 1:150.04", "A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957", 150, 150, null, null, 2350403211, 2054073465, 2083044327, 2326181188, 354957, "DRX305192", "DRS231987", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95287, 0.95643, 0.0891, 0.08586, 0.70309, 0.70252, 0.46384, 0.46281, 151, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [9, "DRR315799", "DRX305191", "DRS231986", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample1", "SAMD00400820", null, "sample name:rw147 2.5dpf wildtype rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400820", "DRX305191", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400820", null, null, null, 10491955578.0, 34900682.0, "DRR315799", "0:150.34 1:150.28", "A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831", 150, 150, null, null, 2796521111, 2446218287, 2483414564, 2765477785, 323831, "DRX305191", "DRS231986", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.9539, 0.95646, 0.08185, 0.07808, 0.70025, 0.70013, 0.44713, 0.44987, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [10, "DRR315798", "DRX305190", "DRS231985", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample4", "SAMD00400819", null, "sample name:rw147 2.5dpf Mutant rep 4|biological replicate:4", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400819", "DRX305190", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400819", null, null, null, 9197802250.0, 30604326.0, "DRR315798", "0:150.30 1:150.24", "A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028", 150, 150, null, null, 2468967963, 2130949980, 2158692262, 2438931017, 261028, "DRX305190", "DRS231985", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95159, 0.95439, 0.10146, 0.09758, 0.71995, 0.71983, 0.46519, 0.46797, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [11, "DRR315797", "DRX305189", "DRS231984", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample3", "SAMD00400818", null, "sample name:rw147 2.5dpf Mutant rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400818", "DRX305189", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400818", null, null, null, 10498982078.0, 34931731.0, "DRR315797", "0:150.31 1:150.25", "A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945", 150, 150, null, null, 2804535103, 2445295179, 2478768789, 2770066062, 316945, "DRX305189", "DRS231984", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95448, 0.95652, 0.0939, 0.0887, 0.71796, 0.71847, 0.46335, 0.46615, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [12, "DRR315796", "DRX305188", "DRS231983", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample2", "SAMD00400817", null, "sample name:rw147 2.5dpf Mutant rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400817", "DRX305188", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400817", null, null, null, 9850145990.0, 32782079.0, "DRR315796", "0:150.26 1:150.21", "A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024", 150, 150, null, null, 2636205537, 2286508705, 2319481100, 2607600624, 350024, "DRX305188", "DRS231983", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95193, 0.95472, 0.09722, 0.09375, 0.7138, 0.71299, 0.45542, 0.45994, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [13, "DRR315795", "DRX305187", "DRS231982", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample1", "SAMD00400816", null, "sample name:rw147 2.5dpf Mutant rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400816", "DRX305187", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "1510Application ReadForward11Application ReadReverse76", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400816", null, null, null, 9542039835.0, 31780260.0, "DRR315795", "0:150.15 1:150.10", "A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225", 150, 150, null, null, 2543384204, 2224374632, 2258183435, 2515655339, 442225, "DRX305187", "DRS231982", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.9528, 0.95591, 0.08656, 0.0828, 0.70352, 0.70331, 0.45316, 0.44914, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [41, "DRR408245", "DRX393851", "DRS407176", "DRP012042", "PRJDB14275", "Zebrafish EN/ENCDC RNA seq", "DRP012042", "Transcriptome Analysis", "A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 3", "zebrafish EN replicate 3", "SAMD00529465", null, "sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529465", "DRX393851", "190326ENvsNC N703 5day;EntericNeuron;rep3", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "NextSeq 550", "1600Application ReadForward11Application ReadReverse81", "DRP012042", "NextSeq 550 paired end sequencing of SAMD00529465", null, null, null, 3729799291.0, 23985772.0, "DRR408245", "0:77.75 1:77.75", "A:978752781;C:879988139;G:903976580;T:962122970;N:4958821", 77, 77, null, null, 978752781, 879988139, 903976580, 962122970, 4958821, "DRX393851", "DRS407176", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [42, "DRR408244", "DRX393850", "DRS407175", "DRP012042", "PRJDB14275", "Zebrafish EN/ENCDC RNA seq", "DRP012042", "Transcriptome Analysis", "A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 2", "zebrafish EN replicate 2", "SAMD00529464", null, "sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529464", "DRX393850", "190326ENvsNC N702 5day;EntericNeuron;rep2", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "NextSeq 550", "1600Application ReadForward11Application ReadReverse81", "DRP012042", "NextSeq 550 paired end sequencing of SAMD00529464", null, null, null, 3315994810.0, 21477755.0, "DRR408244", "0:77.19 1:77.20", "A:873970427;C:778042505;G:798459853;T:859611841;N:5910184", 77, 77, null, null, 873970427, 778042505, 798459853, 859611841, 5910184, "DRX393850", "DRS407175", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [43, "DRR408243", "DRX393849", "DRS407174", "DRP012042", "PRJDB14275", "Zebrafish EN/ENCDC RNA seq", "DRP012042", "Transcriptome Analysis", "A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 1", "zebrafish EN replicate 1", "SAMD00529463", null, "sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529463", "DRX393849", "190326ENvsNC N701 5day;EntericNeuron;rep1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "NextSeq 550", "1600Application ReadForward11Application ReadReverse81", "DRP012042", "NextSeq 550 paired end sequencing of SAMD00529463", null, null, null, 2999501518.0, 19455440.0, "DRR408243", "0:77.08 1:77.09", "A:788053541;C:705895776;G:724185148;T:775760738;N:5606315", 77, 77, null, null, 788053541, 705895776, 724185148, 775760738, 5606315, "DRX393849", "DRS407174", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [312, "ERR977399", "ERX1054382", "ERS805483", "ERP011343", "PRJEB10137", "RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48", "Other", "Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal \u2013 non diabetic \u2013 animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.", null, null, null, "Ductal cells R3", "SAMEA3498334", "GIGA-R, University of Liege", "ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498334|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:3|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:3|strain:Tgnkx6.1:GPF", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 3", "unspecified", "1", "nextera XT", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011343", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16", "NGS14-B703_nkx2_TCCTGAGC_L003_R1_001.fastq.gz NGS14-B703_nkx2_TCCTGAGC_L003_R2_001.fastq.gz", "fastq fastq", 14253683247.0, 70913847.0, "ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 3", "0:101 1:100", "A:3767730088;C:2759135663;G:2772107550;T:3905748607;N:1048961339", 101, 100, null, null, 3767730088, 2759135663, 2772107550, 3905748607, 1048961339, "ERX1054382", "ERS805483", "ERA463457", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.74612, 0.7459, 0.10937, 0.11122, 0.81704, 0.81913, 0.54841, 0.53764, 101, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [313, "ERR977398", "ERX1054381", "ERS805482", "ERP011343", "PRJEB10137", "RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48", "Other", "Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal \u2013 non diabetic \u2013 animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.", null, null, null, "Ductal cells R2", "SAMEA3498333", "GIGA-R, University of Liege", "ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498333|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:2|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:2|strain:Tgnkx6.1:GPF", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 2", "unspecified", "1", "Truseq nano DNAsample", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011343", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16", "NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R2_001.fastq.gz NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R1_001.fastq.gz", "fastq fastq", 17434323262.0, 86308531.0, "ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 2", "0:101 1:101", "A:5014046305;C:3245710338;G:3382410145;T:5701198546;N:90957928", 101, 101, null, null, 5014046305, 3245710338, 3382410145, 5701198546, 90957928, "ERX1054381", "ERS805482", "ERA463457", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.87938, 0.83068, 0.30659, 0.31351, 0.80162, 0.8438, 0.50285, 0.47987, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [314, "ERR977397", "ERX1054380", "ERS805481", "ERP011343", "PRJEB10137", "RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48", "Other", "Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal \u2013 non diabetic \u2013 animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.", null, null, null, "Ductal cells R1", "SAMEA3498332", "GIGA-R, University of Liege", "ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498332|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:1|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:1|strain:Tgnkx6.1:GPF", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 1", "unspecified", "1", "Truseq nano DNA sample", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011343", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16", "NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R1_001.fastq.gz NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R2_001.fastq.gz", "fastq fastq", 8147922500.0, 40336250.0, "ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 1", "0:101 1:101", "A:2422471356;C:1435392327;G:1491979725;T:2755195660;N:42883432", 101, 101, null, null, 2422471356, 1435392327, 1491979725, 2755195660, 42883432, "ERX1054380", "ERS805481", "ERA463457", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.85302, 0.79849, 0.41437, 0.41711, 0.83871, 0.87012, 0.48354, 0.50046, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [315, "ERR1675931", "ERX1745976", "ERS805781", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a \u00df and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R2 1", "SAMEA3498632", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498632|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:37|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:37", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R University of Liege 06 10 2016 15:53:35:325 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "A028_tefa_acinar_GTCCGC_L006_R1_001.fastq.gz A028_tefa_acinar_GTCCGC_L006_R2_001.fastq.gz", "fastq fastq", 10323596830.0, 51106915.0, "ena RUN GIGA R University of Liege 06 10 2016 15:53:35:325 1", "0:101 1:101", "A:2531431314;C:2448656972;G:2434247998;T:2833404838;N:75855708", 101, 101, null, null, 2531431314, 2448656972, 2434247998, 2833404838, 75855708, "ERX1745976", "ERS805781", "ERA727496", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.86878, 0.78451, 0.03164, 0.02157, 0.95077, 0.96161, 0.52068, 0.26664, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [316, "ERR977594", "ERX1054577", "ERS805784", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a \u00df and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R4", "SAMEA3498635", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498635|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:40|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:40", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 19", "Acinar R4", "1", "Truseq nano DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "NGS14-B702_Acinar4_GTGAAA_L008_R1_001.fastq.gz NGS14-B702_Acinar4_GTGAAA_L008_R2_001.fastq.gz", "fastq fastq", 16935208936.0, 83837668.0, "ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 19", "0:101 1:101", "A:4069193994;C:3974803883;G:4029409265;T:4779969672;N:81832122", 101, 101, null, null, 4069193994, 3974803883, 4029409265, 4779969672, 81832122, "ERX1054577", "ERS805784", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.93976, 0.89939, 0.01468, 0.01416, 0.93801, 0.94795, 0.50718, 0.50041, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [317, "ERR977593", "ERX1054576", "ERS805783", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a \u00df and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R3", 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Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.81689, 0.79405, 0.13796, 0.14503, 0.76583, 0.78535, 0.40729, 0.42815, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [328, "ERR977582", "ERX1054565", "ERS805771", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a \u00df and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Alpha cells from adults purified by FACS", "Alpha cells R1 2", "SAMEA3498622", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498622|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:27|cell type:Pancreatic Alpha cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:27", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 7", "Alpha R1 2", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "A083_Alpha1cDNA_ACAGTG_L006_R1_001.fastq.gz A083_Alpha1cDNA_ACAGTG_L006_R2_001.fastq.gz", "fastq fastq", 8598483904.0, 42566752.0, "ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 7", "0:101 1:101", "A:2424152802;C:1756999772;G:1780718036;T:2571949581;N:64663713", 101, 101, null, null, 2424152802, 1756999772, 1780718036, 2571949581, 64663713, "ERX1054565", "ERS805771", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.80654, 0.78693, 0.13676, 0.14263, 0.76475, 0.78173, 0.4476, 0.44884, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [329, "ERR977581", "ERX1054564", "ERS805770", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a \u00df and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Alpha cells from adults purified by FACS", "Alpha cells R1 1", "SAMEA3498621", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498621|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:26|cell type:Pancreatic Alpha cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:26|strain:Tggcga:GFP; Tgins:NTR mCherry", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 6", "Alpha R1 1", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "Alpha1_cDNA_A083_ACAGTG_L003_R2_001.fastq.gz Alpha1_cDNA_A083_ACAGTG_L003_R1_001.fastq.gz", "fastq fastq", 7584054852.0, 37544826.0, "ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 6", "0:101 1:101", "A:2134120600;C:1561394450;G:1604139016;T:2283553056;N:847730", 101, 101, null, null, 2134120600, 1561394450, 1604139016, 2283553056, 847730, "ERX1054564", "ERS805770", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.8102, 0.79183, 0.13509, 0.1414, 0.76459, 0.77958, 0.44897, 0.42232, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [9337, "ERR2865439", "ERX2871399", "ERS2871019", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "sibling 3", "SAMEA5059848", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059848|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling3|common name:zebrafish|sample name:ele sibling3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_sib_F_CTTGTA_L004_R2_001.fastq.gz ele_sib_F_CTTGTA_L004_R1_001.fastq.gz", "fastq fastq", 2823621200.0, 14118106.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6", "0:100 1:100", "A:752781583;C:663838191;G:656422705;T:750213027;N:365694", 100, 100, null, null, 752781583, 663838191, 656422705, 750213027, 365694, "ERX2871399", "ERS2871019", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.95595, 0.95486, 0.09407, 0.09431, 0.67529, 0.67673, 0.45173, 0.44515, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9338, "ERR2865438", "ERX2871398", "ERS2871018", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "sibling 2", "SAMEA5059847", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059847|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling2|common name:zebrafish|sample name:ele sibling2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_sib_D_GCCAAT_L004_R1_001.fastq.gz ele_sib_D_GCCAAT_L004_R2_001.fastq.gz", "fastq fastq", 4217962600.0, 21089813.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5", "0:100 1:100", "A:1119324653;C:996982862;G:984906708;T:1116209552;N:538825", 100, 100, null, null, 1119324653, 996982862, 984906708, 1116209552, 538825, "ERX2871398", "ERS2871018", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.95341, 0.95274, 0.09215, 0.09238, 0.67296, 0.67493, 0.46185, 0.4648, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9339, "ERR2865437", "ERX2871397", "ERS2871017", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "sibling 1", "SAMEA5059846", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059846|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling1|common name:zebrafish|sample name:ele sibling1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_sib_B_TGACCA_L004_R1_001.fastq.gz ele_sib_B_TGACCA_L004_R2_001.fastq.gz", "fastq fastq", 5241628000.0, 26208140.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4", "0:100 1:100", "A:1393802799;C:1235804455;G:1219328189;T:1392021956;N:670601", 100, 100, null, null, 1393802799, 1235804455, 1219328189, 1392021956, 670601, "ERX2871397", "ERS2871017", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.95296, 0.95133, 0.10275, 0.1028, 0.67018, 0.67146, 0.46488, 0.46482, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9340, "ERR2865436", "ERX2871396", "ERS2871016", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "mutant3", "SAMEA5059845", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059845|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant3|common name:zebrafish|sample name:ele mutant3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_E_CAGATC_L004_R1_001.fastq.gz ele_E_CAGATC_L004_R2_001.fastq.gz", "fastq fastq", 3529752000.0, 17648760.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3", "0:100 1:100", "A:933354224;C:837396695;G:828677816;T:929860782;N:462483", 100, 100, null, null, 933354224, 837396695, 828677816, 929860782, 462483, "ERX2871396", "ERS2871016", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.95621, 0.95302, 0.08584, 0.08536, 0.67048, 0.67146, 0.46615, 0.46682, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9341, "ERR2865435", "ERX2871395", "ERS2871015", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "mutant2", "SAMEA5059844", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059844|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant2|common name:zebrafish|sample name:ele mutant2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_C_ACAGTG_L004_R1_001.fastq.gz ele_C_ACAGTG_L004_R2_001.fastq.gz", "fastq fastq", 3119723800.0, 15598619.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2", "0:100 1:100", "A:828335602;C:736691663;G:727853394;T:826449133;N:394008", 100, 100, null, null, 828335602, 736691663, 727853394, 826449133, 394008, "ERX2871395", "ERS2871015", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.94967, 0.94864, 0.0992, 0.09955, 0.65928, 0.66014, 0.47042, 0.46835, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9342, "ERR2865434", "ERX2871394", "ERS2871014", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "mutant1", "SAMEA5059843", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059843|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant1|common name:zebrafish|sample name:ele mutant1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:716 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_A_CGATGT_L004_R1_001.fastq.gz ele_A_CGATGT_L004_R2_001.fastq.gz", "fastq fastq", 2181939600.0, 10909698.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 1", "0:100 1:100", "A:578028200;C:516249107;G:510965740;T:576417363;N:279190", 100, 100, null, null, 578028200, 516249107, 510965740, 576417363, 279190, "ERX2871394", "ERS2871014", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.94968, 0.94939, 0.1131, 0.11293, 0.66245, 0.66251, 0.46654, 0.47475, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9951, "ERR5961093", "ERX5601614", "ERS6490233", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the same batch.", "Uninjected2", "Uninjected2", null, "ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14", null, null, null, null, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8", null, null, null, null, null, null, null, null, null, null, null, "ERX5601614", null, "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9952, "ERR5961092", "ERX5601613", "ERS6490232", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the same batch.", "Uninjected1", "SAMEA8805898", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 06 23|ENA last update:2021 06 23|External Id:SAMEA8805898|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 06 23T08:18:31Z|INSDC last update:2021 06 23T08:18:31Z|INSDC status:public|Submitter Id:Uninjected1|common name:zebrafish|sample name:Uninjected1", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 06 23|ENA LAST UPDATE:2021 06 23", "WT1_R1_001.fastq WT1_R2_001.fastq", "fastq fastq", 5664550800.0, 18881836.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7", "0:150 1:150", "A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763", 150, 150, null, null, 1493322675, 1337347146, 1388414458, 1444981758, 484763, "ERX5601613", "ERS6490232", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95769, 0.95822, 0.04407, 0.04391, 0.69934, 0.69958, 0.4411, 0.45319, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9953, "ERR5961096", "ERX5601617", "ERS6490236", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the an additional batch.", "Uninjected5", "SAMEA8805902", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805902|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected5|common name:zebrafish|sample name:Uninjected5", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "WT5_R1_001.fastq.gz WT5_R2_001.fastq.gz", "fastq fastq", 9088444200.0, 30294814.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11", "0:150 1:150", "A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622", 150, 150, null, null, 2404715160, 2098546919, 2330441921, 2254532578, 207622, "ERX5601617", "ERS6490236", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95076, 0.93857, 0.06296, 0.06222, 0.68485, 0.70047, 0.47429, 0.48524, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9954, "ERR5961095", "ERX5601616", "ERS6490235", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the an additional batch.", "Uninjected4", "SAMEA8805901", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805901|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected4|common name:zebrafish|sample name:Uninjected4", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "WT4_R1_001.fastq.gz WT4_R2_001.fastq.gz", "fastq fastq", 9222083700.0, 30740279.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10", "0:150 1:150", "A:2328864269;C:2117919914;G:2560286870;T:2214801519;N:211128", 150, 150, null, null, 2328864269, 2117919914, 2560286870, 2214801519, 211128, "ERX5601616", "ERS6490235", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95124, 0.92695, 0.05122, 0.05036, 0.69118, 0.70634, 0.47769, 0.47806, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9955, "ERR5961094", "ERX5601615", "ERS6490234", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the an additional batch.", "Uninjected3", "SAMEA8805900", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805900|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected3|common name:zebrafish|sample name:Uninjected3", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "WT3_R1_001.fastq.gz WT3_R2_001.fastq.gz", "fastq fastq", 9088444200.0, 30294814.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9", "0:150 1:150", "A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622", 150, 150, null, null, 2404715160, 2098546919, 2330441921, 2254532578, 207622, "ERX5601615", "ERS6490234", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95071, 0.93855, 0.06295, 0.06183, 0.68511, 0.70065, 0.47621, 0.48573, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9956, "ERR5961091", "ERX5601612", "ERS6490231", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.", "Cas9enzyme3", "SAMEA8805897", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805897|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme3|common name:zebrafish|sample name:Cas9enzyme3", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "RNA3_R1_001.fastq RNA3_R2_001.fastq", "fastq fastq", 5814764400.0, 19382548.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6", "0:150 1:150", "A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867", 150, 150, null, null, 1550014255, 1359566801, 1419514658, 1485169819, 498867, "ERX5601612", "ERS6490231", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.96166, 0.96182, 0.04962, 0.04954, 0.68172, 0.68144, 0.45683, 0.46611, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9957, "ERR5961090", "ERX5601611", "ERS6490230", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.", "Cas9enzyme2", "SAMEA8805896", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805896|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme2|common name:zebrafish|sample name:Cas9enzyme2", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "RNA2_R1_001.fastq RNA2_R2_001.fastq", "fastq fastq", 5927606100.0, 19758687.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5", "0:150 1:150", "A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534", 150, 150, null, null, 1579767222, 1387675810, 1439122138, 1520529396, 511534, "ERX5601611", "ERS6490230", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.96217, 0.96214, 0.05174, 0.05176, 0.67083, 0.6716, 0.46772, 0.47128, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9958, "ERR5961089", "ERX5601610", "ERS6490229", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.", "Cas9enzyme1", "SAMEA8805895", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805895|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme1|common name:zebrafish|sample name:Cas9enzyme1", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "RNA1_R1_001.fastq RNA1_R2_001.fastq", "fastq fastq", 5738133000.0, 19127110.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4", "0:150 1:150", "A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691", 150, 150, null, null, 1530616107, 1342298453, 1401357126, 1463360623, 500691, "ERX5601610", "ERS6490229", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95709, 0.9569, 0.05132, 0.05149, 0.68771, 0.68846, 0.45988, 0.47329, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9959, "ERR5961088", "ERX5601609", "ERS6490228", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.", "Cas9mRNA3", "SAMEA8805894", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805894|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA3|common name:zebrafish|sample name:Cas9mRNA3", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "PRO3_R1_001.fastq PRO3_R2_001.fastq", "fastq fastq", 9635841900.0, 32119473.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3", "0:150 1:150", "A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911", 150, 150, null, null, 2562857735, 2253487693, 2325345541, 2493627020, 523911, "ERX5601609", "ERS6490228", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95769, 0.95696, 0.05441, 0.05397, 0.67424, 0.67407, 0.46338, 0.46444, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9960, "ERR5961087", "ERX5601608", "ERS6490227", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.", "Cas9mRNA2", "SAMEA8805893", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805893|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA2|common name:zebrafish|sample name:Cas9mRNA2", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 10 21", "PRO2_R1_001.fastq PRO2_R2_001.fastq", "fastq fastq", 8990649900.0, 29968833.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2", "0:150 1:150", "A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619", 150, 150, null, null, 2370044440, 2140400380, 2185347925, 2294361536, 495619, "ERX5601608", "ERS6490227", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95444, 0.95397, 0.05839, 0.05842, 0.67377, 0.67207, 0.48505, 0.48043, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9961, "ERR5961086", "ERX5601607", "ERS6490226", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.", "Cas9mRNA1", "SAMEA8805892", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805892|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA1|common name:zebrafish|sample name:Cas9mRNA1", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "PRO1_R1_001.fastq PRO1_R2_001.fastq", "fastq fastq", 8803789500.0, 29345965.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1", "0:150 1:150", "A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952", 150, 150, null, null, 2318913314, 2090675347, 2149054140, 2244296747, 849952, "ERX5601607", "ERS6490226", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.954, 0.9549, 0.04652, 0.04639, 0.70806, 0.71386, 0.45393, 0.44921, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9962, "ERR4902960", "ERX4769932", "ERS5427208", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected.", "CRISPR RNAseq", "SAMEA7670216", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670216|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:12Z|INSDC status:public|Submitter Id:CRISPR RNAseq8|common name:zebrafish|sample name:CRISPR RNAseq8", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "WT2_R1_001.fastq.gz WT2_R2_001.fastq.gz", "fastq fastq", 7020700500.0, 23402335.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8", "0:150 1:150", "A:1879937256;C:1626166066;G:1693802223;T:1820178560;N:616395", 150, 150, null, null, 1879937256, 1626166066, 1693802223, 1820178560, 616395, "ERX4769932", "ERS5427208", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.92352, 0.92388, 0.04778, 0.04768, 0.6924, 0.69205, 0.45557, 0.45865, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9963, "ERR4902959", "ERX4769931", "ERS5427206", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected.", "CRISPR RNAseq", "SAMEA7670214", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670214|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq7|common name:zebrafish|sample name:CRISPR RNAseq7", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "WT1_R1_001.fastq.gz WT1_R2_001.fastq.gz", "fastq fastq", 5664550800.0, 18881836.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7", "0:150 1:150", "A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763", 150, 150, null, null, 1493322675, 1337347146, 1388414458, 1444981758, 484763, "ERX4769931", "ERS5427206", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95767, 0.95821, 0.04411, 0.04384, 0.69944, 0.69944, 0.44168, 0.45263, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9964, "ERR4902958", "ERX4769930", "ERS5427204", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.", "CRISPR RNAseq", "SAMEA7670212", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670212|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq6|common name:zebrafish|sample name:CRISPR RNAseq6", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "RNA3_R1_001.fastq.gz RNA3_R2_001.fastq.gz", "fastq fastq", 5814764400.0, 19382548.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 6", "0:150 1:150", "A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867", 150, 150, null, null, 1550014255, 1359566801, 1419514658, 1485169819, 498867, "ERX4769930", "ERS5427204", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.96165, 0.96177, 0.04961, 0.04952, 0.68183, 0.68142, 0.45636, 0.46565, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9965, "ERR4902957", "ERX4769929", "ERS5427203", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.", "CRISPR RNAseq", "SAMEA7670211", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670211|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq5|common name:zebrafish|sample name:CRISPR RNAseq5", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "RNA2_R1_001.fastq.gz RNA2_R2_001.fastq.gz", "fastq fastq", 5927606100.0, 19758687.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 5", "0:150 1:150", "A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534", 150, 150, null, null, 1579767222, 1387675810, 1439122138, 1520529396, 511534, "ERX4769929", "ERS5427203", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.96212, 0.96213, 0.0519, 0.05167, 0.67099, 0.6715, 0.46875, 0.47089, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9966, "ERR4902956", "ERX4769928", "ERS5427201", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.", "CRISPR RNAseq", "SAMEA7670209", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670209|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq4|common name:zebrafish|sample name:CRISPR RNAseq4", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "RNA1_R1_001.fastq.gz RNA1_R2_001.fastq.gz", "fastq fastq", 5738133000.0, 19127110.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 4", "0:150 1:150", "A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691", 150, 150, null, null, 1530616107, 1342298453, 1401357126, 1463360623, 500691, "ERX4769928", "ERS5427201", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95706, 0.9569, 0.05122, 0.05151, 0.68757, 0.68822, 0.46039, 0.4732, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9967, "ERR4902955", "ERX4769927", "ERS5427199", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.", "CRISPR RNAseq", "SAMEA7670207", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670207|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq3|common name:zebrafish|sample name:CRISPR RNAseq3", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "PRO3_R1_001.fastq.gz PRO3_R2_001.fastq.gz", "fastq fastq", 9635841900.0, 32119473.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 3", "0:150 1:150", "A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911", 150, 150, null, null, 2562857735, 2253487693, 2325345541, 2493627020, 523911, "ERX4769927", "ERS5427199", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95766, 0.95695, 0.05445, 0.05404, 0.67432, 0.67403, 0.46385, 0.46442, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9968, "ERR4902954", "ERX4769926", "ERS5427197", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.", "CRISPR RNAseq", "SAMEA7670205", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670205|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq2|common name:zebrafish|sample name:CRISPR RNAseq2", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "PRO2_R1_001.fastq.gz PRO2_R2_001.fastq.gz", "fastq fastq", 8990649900.0, 29968833.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 2", "0:150 1:150", "A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619", 150, 150, null, null, 2370044440, 2140400380, 2185347925, 2294361536, 495619, "ERX4769926", "ERS5427197", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95444, 0.95393, 0.05848, 0.05894, 0.67438, 0.67255, 0.4825, 0.48028, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9969, "ERR4902953", "ERX4769925", "ERS5427195", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.", "CRISPR RNAseq", "SAMEA7670203", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670203|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq1|common name:zebrafish|sample name:CRISPR RNAseq1", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "PRO1_R1_001.fastq.gz PRO1_R2_001.fastq.gz", "fastq fastq", 8803789500.0, 29345965.0, "ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 1", "0:150 1:150", "A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952", 150, 150, null, null, 2318913314, 2090675347, 2149054140, 2244296747, 849952, "ERX4769925", "ERS5427195", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95403, 0.95489, 0.04655, 0.0464, 0.70816, 0.71403, 0.45357, 0.44874, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [10383, "ERR8517249", "ERX8083723", "ERS10517669", "ERP135370", "PRJEB50765", "HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS", "69e2093b-755e-4be3-88b8-5b4a761258fe", "Other", "A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD.", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "PUBMED:29302778;PUBMED:35895140", "Modifier control", "hnRNPK 003", "SAMEA12918519", "vib-ku leuven", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918519|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 003|common name:zebrafish|sample name:hnRNPK 003", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Raw reads: hnRNPK 003", "webin reads hnRNPK 003", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135370", "Raw reads: hnRNPK 003", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "hnRNPK_003_R1.fastq.gz hnRNPK_003_R2.fastq.gz", "fastq fastq", 2931486932.0, 19421721.0, "webin reads hnRNPK 003", "0:75.51 1:75.43", "A:759548162;C:700272829;G:700149526;T:770783019;N:733396", 75, 75, null, null, 759548162, 700272829, 700149526, 770783019, 733396, "ERX8083723", "ERS10517669", "ERA8937191", "vib-ku leuven|European Nucleotide Archive", "vib-ku leuven", 2, 0.9621, 0.96378, 0.06994, 0.06876, 0.68757, 0.68998, 0.46746, 0.47041, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2022-08-22", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [10384, "ERR8517226", "ERX8083700", "ERS10517665", "ERP135370", "PRJEB50765", "HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS", "69e2093b-755e-4be3-88b8-5b4a761258fe", "Other", "A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD.", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "PUBMED:29302778;PUBMED:35895140", "Modifier control", "hnRNPK 001", "SAMEA12918515", "vib-ku leuven", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918515|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 001|common name:zebrafish|sample name:hnRNPK 001", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Raw reads: hnRNPK 001", "webin reads hnRNPK 001", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135370", "Raw reads: hnRNPK 001", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "hnRNPK_001_R1.fastq.gz hnRNPK_001_R2.fastq.gz", "fastq fastq", 2728299749.0, 18074835.0, "webin reads hnRNPK 001", "0:75.51 1:75.43", "A:710869412;C:649804308;G:644363972;T:722599378;N:662679", 75, 75, null, null, 710869412, 649804308, 644363972, 722599378, 662679, "ERX8083700", "ERS10517665", "ERA8936710", "vib-ku leuven|European Nucleotide Archive", "vib-ku leuven", 2, 0.96092, 0.96336, 0.07296, 0.07144, 0.68862, 0.69209, 0.47036, 0.47104, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2022-08-22", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [10385, "ERR8517194", "ERX8083668", "ERS10517668", "ERP135370", "PRJEB50765", "HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS", "69e2093b-755e-4be3-88b8-5b4a761258fe", "Other", "A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD.", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "PUBMED:29302778;PUBMED:35895140", "RNA control", "GFP 003", "SAMEA12918518", "vib-ku leuven", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918518|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 003|common name:zebrafish|sample name:GFP 003", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Raw reads: GFP 003", "webin reads GFP 003", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135370", "Raw reads: GFP 003", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "GFP_003_R1.fastq.gz GFP_003_R2.fastq.gz", "fastq fastq", 2845571506.0, 18850866.0, "webin reads GFP 003", "0:75.52 1:75.43", "A:737412560;C:678774596;G:684567775;T:744108157;N:708418", 75, 75, null, null, 737412560, 678774596, 684567775, 744108157, 708418, "ERX8083668", "ERS10517668", "ERA8936242", "vib-ku leuven|European Nucleotide Archive", "vib-ku leuven", 2, 0.96279, 0.96355, 0.06774, 0.06607, 0.68864, 0.69183, 0.469, 0.46906, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2022-08-22", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [10386, "ERR8517159", "ERX8083633", "ERS10517664", "ERP135370", "PRJEB50765", "HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS", "69e2093b-755e-4be3-88b8-5b4a761258fe", "Other", "A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD.", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "PUBMED:29302778;PUBMED:35895140", "RNA control", "GFP 001", "SAMEA12918514", "vib-ku leuven", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918514|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 001|common name:zebrafish|sample name:GFP 001", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Raw reads: GFP 001", "webin reads GFP 001", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135370", "Raw reads: GFP 001", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "GFP_001_R1.fastq.gz GFP_001_R2.fastq.gz", "fastq fastq", 2873485447.0, 19035162.0, "webin reads GFP 001", "0:75.52 1:75.44", "A:746120172;C:687054955;G:682142981;T:757435799;N:731540", 75, 75, null, null, 746120172, 687054955, 682142981, 757435799, 731540, "ERX8083633", "ERS10517664", "ERA8935703", "vib-ku leuven|European Nucleotide Archive", "vib-ku leuven", 2, 0.96176, 0.96461, 0.07014, 0.06932, 0.68672, 0.68913, 0.47006, 0.46794, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2022-08-22", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [10387, "ERR8517115", "ERX8083589", "ERS10517671", "ERP135370", "PRJEB50765", "HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS", "69e2093b-755e-4be3-88b8-5b4a761258fe", "Other", "A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD.", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "PUBMED:29302778;PUBMED:35895140", "Modifier rescue", "91S hnRNPK 003", "SAMEA12918521", "vib-ku leuven", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918521|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 003|common name:zebrafish|sample name:91S hnRNPK 003", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 003", "webin reads 91S hnRNPK 003", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135370", "Raw reads: 91S hnRNPK 003", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "91S_hnRNPK_003_R1.fastq.gz 91S_hnRNPK_003_R2.fastq.gz", "fastq fastq", 2853403405.0, 18902398.0, "webin reads 91S hnRNPK 003", "0:75.52 1:75.44", "A:739541111;C:681340573;G:681790014;T:750013318;N:718389", 75, 75, null, null, 739541111, 681340573, 681790014, 750013318, 718389, "ERX8083589", "ERS10517671", "ERA8935191", "vib-ku leuven|European Nucleotide Archive", "vib-ku leuven", 2, 0.96234, 0.96429, 0.0679, 0.06627, 0.68984, 0.69126, 0.46434, 0.47087, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2022-08-22", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [10388, "ERR8517082", "ERX8083556", "ERS10517667", "ERP135370", "PRJEB50765", "HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS", "69e2093b-755e-4be3-88b8-5b4a761258fe", "Other", "A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD.", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "PUBMED:29302778;PUBMED:35895140", "Modifier rescue", "91S hnRNPK 001", "SAMEA12918517", "vib-ku leuven", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918517|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 001|common name:zebrafish|sample name:91S hnRNPK 001", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 001", "webin reads 91S hnRNPK 001", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135370", "Raw reads: 91S hnRNPK 001", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "91S_hnRNPK_001_R1.fastq.gz 91S_hnRNPK_001_R2.fastq.gz", "fastq fastq", 2795603091.0, 18519699.0, "webin reads 91S hnRNPK 001", "0:75.52 1:75.43", "A:722724564;C:672552332;G:664566386;T:735058575;N:701234", 75, 75, null, null, 722724564, 672552332, 664566386, 735058575, 701234, "ERX8083556", "ERS10517667", "ERA8934579", "vib-ku leuven|European Nucleotide Archive", "vib-ku leuven", 2, 0.96307, 0.96547, 0.06551, 0.06458, 0.68714, 0.68856, 0.46817, 0.46555, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2022-08-22", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [10389, "ERR8517039", "ERX8083513", "ERS10517670", "ERP135370", "PRJEB50765", "HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS", "69e2093b-755e-4be3-88b8-5b4a761258fe", "Other", "A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD.", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "PUBMED:29302778;PUBMED:35895140", "Toxic condition", "91S GFP 003", "SAMEA12918520", "vib-ku leuven", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918520|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 003|common name:zebrafish|sample name:91S GFP 003", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Raw reads: 91S GFP 003", "webin reads 91S GFP 003", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135370", "Raw reads: 91S GFP 003", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "91S_GFP_003_R1.fastq.gz 91S_GFP_003_R2.fastq.gz", "fastq fastq", 2946600193.0, 19521826.0, "webin reads 91S GFP 003", "0:75.51 1:75.43", "A:763284580;C:704439363;G:702989767;T:775149110;N:737373", 75, 75, null, null, 763284580, 704439363, 702989767, 775149110, 737373, "ERX8083513", "ERS10517670", "ERA8933888", "vib-ku leuven|European Nucleotide Archive", "vib-ku leuven", 2, 0.96151, 0.96295, 0.06621, 0.06481, 0.68807, 0.69092, 0.46928, 0.46982, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2022-08-22", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [10390, "ERR8516998", "ERX8083472", "ERS10517666", "ERP135370", "PRJEB50765", "HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS", "69e2093b-755e-4be3-88b8-5b4a761258fe", "Other", "A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD.", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "PUBMED:29302778;PUBMED:35895140", "Toxic condition", "91S GFP 001", "SAMEA12918516", "vib-ku leuven", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918516|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 001|common name:zebrafish|sample name:91S GFP 001", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Raw reads: 91S GFP 001", "webin reads 91S GFP 001", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP135370", "Raw reads: 91S GFP 001", "ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22", "91S_GFP_001_R1.fastq.gz 91S_GFP_001_R2.fastq.gz", "fastq fastq", 2821113913.0, 18686946.0, "webin reads 91S GFP 001", "0:75.52 1:75.44", "A:726676187;C:676899384;G:676400816;T:740427303;N:710223", 75, 75, null, null, 726676187, 676899384, 676400816, 740427303, 710223, "ERX8083472", "ERS10517666", "ERA8933211", "vib-ku leuven|European Nucleotide Archive", "vib-ku leuven", 2, 0.96147, 0.96465, 0.07106, 0.06991, 0.68822, 0.69556, 0.47261, 0.47451, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2022-08-22", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [14875, "ERR12071836", "ERX11454461", "ERS16387703", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E115 1", "SAMEA114399011", "University of East Anglia", "ENA FIRST PUBLIC:2023 10 06T08:31:44Z|ENA LAST UPDATE:2023 10 06T08:31:44Z|External Id:SAMEA114399011|INSDC center name:University of East Anglia|INSDC first public:2023 10 06T08:31:44Z|INSDC last update:2023 10 06T08:31:44Z|INSDC status:public|Submitter Id:115 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66715", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 10 06|ENA LAST UPDATE:2023 10 06", "115-1_S69_L006_R1_001.fastq.gz 115-1_S69_L006_R2_001.fastq.gz", "fastq fastq", 12813280704.0, 50846352.0, "ena RUN TAB 21 09 2023 13:32:15:295 66716", "0:126 1:126", "A:2451295493;C:3891843753;G:4001866488;T:2448421880;N:19853090", 126, 126, null, null, 2451295493, 3891843753, 4001866488, 2448421880, 19853090, "ERX11454461", "ERS16387703", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.89907, 0.8514, 0.17845, 0.173, 0.80369, 0.81085, 0.83252, 0.83449, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14876, "ERR12071855", "ERX11454480", "ERS16387722", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E83 5", "SAMEA114399030", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:83 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:300 66753", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "83-5_S40_L008_R1_001.fastq.gz 83-5_S40_L008_R2_001.fastq.gz", "fastq fastq", 13683493656.0, 54299578.0, "ena RUN TAB 21 09 2023 13:32:15:300 66754", "0:126 1:126", "A:2772843483;C:4073415925;G:4192640412;T:2641952920;N:2640916", 126, 126, null, null, 2772843483, 4073415925, 4192640412, 2641952920, 2640916, "ERX11454480", "ERS16387722", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.92452, 0.92427, 0.15846, 0.16251, 0.7777, 0.77666, 0.78362, 0.77515, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14877, "ERR12071854", "ERX11454479", "ERS16387721", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E83 4", "SAMEA114399029", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:83 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66751", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "83-4_S8_L002_R1_001.fastq.gz 83-4_S8_L002_R2_001.fastq.gz", "fastq fastq", 10045714644.0, 39863947.0, "ena RUN TAB 21 09 2023 13:32:15:300 66752", "0:126 1:126", "A:2037388456;C:2963530056;G:3069663461;T:1972981871;N:2150800", 126, 126, null, null, 2037388456, 2963530056, 3069663461, 1972981871, 2150800, "ERX11454479", "ERS16387721", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.91872, 0.91762, 0.16049, 0.16307, 0.76516, 0.76644, 0.77023, 0.77199, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14878, "ERR12071853", "ERX11454478", "ERS16387720", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E83 3", "SAMEA114399028", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:83 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66749", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "83-3_S12_L003_R1_001.fastq.gz 83-3_S12_L003_R2_001.fastq.gz", "fastq fastq", 17333567748.0, 68783999.0, "ena RUN TAB 21 09 2023 13:32:15:299 66750", "0:126 1:126", "A:3399006637;C:5245167754;G:5416988818;T:3269621086;N:2783453", 126, 126, null, null, 3399006637, 5245167754, 5416988818, 3269621086, 2783453, "ERX11454478", "ERS16387720", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.93044, 0.93099, 0.14459, 0.1479, 0.77287, 0.774, 0.78248, 0.78348, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14879, "ERR12071852", "ERX11454477", "ERS16387719", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E83 1", "SAMEA114399027", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:83 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66747", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "83-1_S4_L001_R1_001.fastq.gz 83-1_S4_L001_R2_001.fastq.gz", "fastq fastq", 14977164132.0, 59433191.0, "ena RUN TAB 21 09 2023 13:32:15:299 66748", "0:126 1:126", "A:3115980365;C:4357431505;G:4531888641;T:2968758582;N:3105039", 126, 126, null, null, 3115980365, 4357431505, 4531888641, 2968758582, 3105039, "ERX11454477", "ERS16387719", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.89622, 0.89549, 0.15698, 0.16074, 0.76558, 0.76779, 0.70301, 0.73129, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14880, "ERR12071851", "ERX11454476", "ERS16387718", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E82 5", "SAMEA114399026", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:82 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66745", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "82-5_S3_L001_R1_001.fastq.gz 82-5_S3_L001_R2_001.fastq.gz", "fastq fastq", 14575744764.0, 57840257.0, "ena RUN TAB 21 09 2023 13:32:15:299 66746", "0:126 1:126", "A:3079286238;C:4161280385;G:4315514217;T:3016549159;N:3114765", 126, 126, null, null, 3079286238, 4161280385, 4315514217, 3016549159, 3114765, "ERX11454476", "ERS16387718", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.82553, 0.82489, 0.15941, 0.16124, 0.77337, 0.77518, 0.73773, 0.75718, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14881, "ERR12071850", "ERX11454475", "ERS16387717", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E82 3", "SAMEA114399025", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:82 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66743", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "82-3_S11_L003_R1_001.fastq.gz 82-3_S11_L003_R2_001.fastq.gz", "fastq fastq", 15753924144.0, 62515572.0, "ena RUN TAB 21 09 2023 13:32:15:299 66744", "0:126 1:126", "A:3294606329;C:4538635184;G:4708756438;T:3209425450;N:2500743", 126, 126, null, null, 3294606329, 4538635184, 4708756438, 3209425450, 2500743, "ERX11454475", "ERS16387717", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.8642, 0.86388, 0.1596, 0.16298, 0.77051, 0.77297, 0.7599, 0.7352, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14882, "ERR12071849", "ERX11454474", "ERS16387716", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E82 2", "SAMEA114399024", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:82 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66741", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 22", "82-2_S7_L002_R1_001.fastq.gz 82-2_S7_L002_R2_001.fastq.gz", "fastq fastq", 20680686684.0, 82066217.0, "ena RUN TAB 21 09 2023 13:32:15:298 66742", "0:126 1:126", "A:4358995918;C:5919331822;G:6101024757;T:4296885228;N:4448959", 126, 126, null, null, 4358995918, 5919331822, 6101024757, 4296885228, 4448959, "ERX11454474", "ERS16387716", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.88722, 0.88591, 0.1721, 0.1755, 0.76207, 0.76394, 0.74661, 0.7483, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14883, "ERR12071848", "ERX11454473", "ERS16387715", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E82 1", "SAMEA114399023", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:82 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66739", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "82-1_S39_L008_R1_001.fastq.gz 82-1_S39_L008_R2_001.fastq.gz", "fastq fastq", 19062862812.0, 75646281.0, "ena RUN TAB 21 09 2023 13:32:15:298 66740", "0:126 1:126", "A:4015412618;C:5485657253;G:5643544062;T:3914646370;N:3602509", 126, 126, null, null, 4015412618, 5485657253, 5643544062, 3914646370, 3602509, "ERX11454473", "ERS16387715", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.82331, 0.82289, 0.14959, 0.15262, 0.77786, 0.77368, 0.75014, 0.71846, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14884, "ERR12071847", "ERX11454472", "ERS16387714", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E81 5", "SAMEA114399022", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:81 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66737", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "81-5_S6_L002_R1_001.fastq.gz 81-5_S6_L002_R2_001.fastq.gz", "fastq fastq", 14105505960.0, 55974230.0, "ena RUN TAB 21 09 2023 13:32:15:298 66738", "0:126 1:126", "A:2867593807;C:4154280778;G:4295901883;T:2784713422;N:3016070", 126, 126, null, null, 2867593807, 4154280778, 4295901883, 2784713422, 3016070, "ERX11454472", "ERS16387714", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.89055, 0.89059, 0.15225, 0.15462, 0.77031, 0.7709, 0.77204, 0.74565, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14885, "ERR12071846", "ERX11454471", "ERS16387713", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E81 4", "SAMEA114399021", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:81 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66735", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "81-4_S38_L008_R1_001.fastq.gz 81-4_S38_L008_R2_001.fastq.gz", "fastq fastq", 14056344540.0, 55779145.0, "ena RUN TAB 21 09 2023 13:32:15:298 66736", "0:126 1:126", "A:2941182079;C:4065026103;G:4178339299;T:2869101906;N:2695153", 126, 126, null, null, 2941182079, 4065026103, 4178339299, 2869101906, 2695153, "ERX11454471", "ERS16387713", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.85089, 0.84987, 0.16263, 0.16502, 0.77837, 0.77283, 0.74931, 0.72487, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14886, "ERR12071845", "ERX11454470", "ERS16387712", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E81 2", "SAMEA114399020", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:81 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66733", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "81-2_S10_L003_R2_001.fastq.gz 81-2_S10_L003_R1_001.fastq.gz", "fastq fastq", 12344567004.0, 48986377.0, "ena RUN TAB 21 09 2023 13:32:15:297 66734", "0:126 1:126", "A:2564870489;C:3577715066;G:3699995887;T:2500054422;N:1931140", 126, 126, null, null, 2564870489, 3577715066, 3699995887, 2500054422, 1931140, "ERX11454470", "ERS16387712", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.81332, 0.81278, 0.14345, 0.14595, 0.77962, 0.78011, 0.77642, 0.76714, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14887, "ERR12071844", "ERX11454469", "ERS16387711", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E81 1", "SAMEA114399019", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:81 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66731", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "81-1_S2_L001_R1_001.fastq.gz 81-1_S2_L001_R2_001.fastq.gz", "fastq fastq", 16863847056.0, 66920028.0, "ena RUN TAB 21 09 2023 13:32:15:297 66732", "0:126 1:126", "A:3484102096;C:4908704805;G:5083802657;T:3383595635;N:3641863", 126, 126, null, null, 3484102096, 4908704805, 5083802657, 3383595635, 3641863, "ERX11454469", "ERS16387711", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.90019, 0.89959, 0.16463, 0.16683, 0.76607, 0.76792, 0.76365, 0.73132, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14888, "ERR12071843", "ERX11454468", "ERS16387710", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E80 4", "SAMEA114399018", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:80 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66729", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "80-4_S9_L003_R1_001.fastq.gz 80-4_S9_L003_R2_001.fastq.gz", "fastq fastq", 22230539604.0, 88216427.0, "ena RUN TAB 21 09 2023 13:32:15:297 66730", "0:126 1:126", "A:4399600032;C:6651638899;G:6855034908;T:4320719496;N:3546269", 126, 126, null, null, 4399600032, 6651638899, 6855034908, 4320719496, 3546269, "ERX11454468", "ERS16387710", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.84585, 0.84448, 0.14327, 0.14586, 0.79078, 0.79251, 0.79803, 0.79459, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14889, "ERR12071842", "ERX11454467", "ERS16387709", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E80 3", "SAMEA114399017", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:80 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66727", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "80-3_S1_L001_R2_001.fastq.gz 80-3_S1_L001_R1_001.fastq.gz", "fastq fastq", 17944230024.0, 71207262.0, "ena RUN TAB 21 09 2023 13:32:15:296 66728", "0:126 1:126", "A:3713490828;C:5207225554;G:5378396527;T:3641393155;N:3723960", 126, 126, null, null, 3713490828, 5207225554, 5378396527, 3641393155, 3723960, "ERX11454467", "ERS16387709", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.84454, 0.84386, 0.14922, 0.15129, 0.77264, 0.77339, 0.75797, 0.76206, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14890, "ERR12071841", "ERX11454466", "ERS16387708", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E80 2", "SAMEA114399016", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:80 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66725", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "80-2_S5_L002_R1_001.fastq.gz 80-2_S5_L002_R2_001.fastq.gz", "fastq fastq", 16641238320.0, 66036660.0, "ena RUN TAB 21 09 2023 13:32:15:296 66726", "0:126 1:126", "A:3508280857;C:4757668643;G:4898009962;T:3473768461;N:3510397", 126, 126, null, null, 3508280857, 4757668643, 4898009962, 3473768461, 3510397, "ERX11454466", "ERS16387708", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.86106, 0.86111, 0.16002, 0.16307, 0.7653, 0.76542, 0.72623, 0.70444, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14891, "ERR12071840", "ERX11454465", "ERS16387707", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E80 1", "SAMEA114399015", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:80 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66723", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "80-1_S37_L008_R1_001.fastq.gz 80-1_S37_L008_R2_001.fastq.gz", "fastq fastq", 15269215248.0, 60592124.0, "ena RUN TAB 21 09 2023 13:32:15:296 66724", "0:126 1:126", "A:3161128702;C:4439474080;G:4571245477;T:3094451760;N:2915229", 126, 126, null, null, 3161128702, 4439474080, 4571245477, 3094451760, 2915229, "ERX11454465", "ERS16387707", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.84008, 0.83924, 0.16203, 0.16482, 0.78486, 0.78301, 0.76847, 0.76451, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14892, "ERR12071839", "ERX11454464", "ERS16387706", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E115 5", "SAMEA114399014", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:115 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66721", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "115-5_S28_L005_R2_001.fastq.gz 115-5_S28_L005_R1_001.fastq.gz", "fastq fastq", 13704997824.0, 54384912.0, "ena RUN TAB 21 09 2023 13:32:15:296 66722", "0:126 1:126", "A:2791048995;C:4040751875;G:4161655954;T:2708992373;N:2548627", 126, 126, null, null, 2791048995, 4040751875, 4161655954, 2708992373, 2548627, "ERX11454464", "ERS16387706", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.92152, 0.922, 0.16432, 0.16746, 0.77977, 0.77723, 0.7658, 0.74319, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14893, "ERR12071838", "ERX11454463", "ERS16387705", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E115 4", "SAMEA114399013", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:115 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66719", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "115-4_S73_L007_R1_001.fastq.gz 115-4_S73_L007_R2_001.fastq.gz", "fastq fastq", 13555374840.0, 53791170.0, "ena RUN TAB 21 09 2023 13:32:15:295 66720", "0:126 1:126", "A:2613879041;C:4131073531;G:4251239682;T:2536011431;N:23171155", 126, 126, null, null, 2613879041, 4131073531, 4251239682, 2536011431, 23171155, "ERX11454463", "ERS16387705", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.93971, 0.93992, 0.15435, 0.15669, 0.78766, 0.79076, 0.76218, 0.78676, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14894, "ERR12071837", "ERX11454462", "ERS16387704", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E115 2", "SAMEA114399012", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:115 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66717", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "115-2_S77_L008_R1_001.fastq.gz 115-2_S77_L008_R2_001.fastq.gz", "fastq fastq", 19309168872.0, 76623686.0, "ena RUN TAB 21 09 2023 13:32:15:295 66718", "0:126 1:126", "A:3659403129;C:5914313547;G:6102556630;T:3596021103;N:36874463", 126, 126, null, null, 3659403129, 5914313547, 6102556630, 3596021103, 36874463, "ERX11454462", "ERS16387704", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.90206, 0.90085, 0.164, 0.16686, 0.81477, 0.81856, 0.84674, 0.83786, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14895, "ERR12071835", "ERX11454460", "ERS16387702", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E114 5", "SAMEA114399010", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:114 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66713", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "114-5_S68_L006_R1_001.fastq.gz 114-5_S68_L006_R2_001.fastq.gz", "fastq fastq", 14161249872.0, 56195436.0, "ena RUN TAB 21 09 2023 13:32:15:295 66714", "0:126 1:126", "A:2927386834;C:4098238005;G:4213138034;T:2900333935;N:22153064", 126, 126, null, null, 2927386834, 4098238005, 4213138034, 2900333935, 22153064, "ERX11454460", "ERS16387702", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.92035, 0.91983, 0.16785, 0.17009, 0.75864, 0.76292, 0.73081, 0.75429, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14896, "ERR12071834", "ERX11454459", "ERS16387701", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E114 4", "SAMEA114399009", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:114 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66711", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "114-4_S76_L008_R1_001.fastq.gz 114-4_S76_L008_R2_001.fastq.gz", "fastq fastq", 12939456600.0, 51347050.0, "ena RUN TAB 21 09 2023 13:32:15:294 66712", "0:126 1:126", "A:2686900916;C:3725092053;G:3826228928;T:2676529407;N:24705296", 126, 126, null, null, 2686900916, 3725092053, 3826228928, 2676529407, 24705296, "ERX11454459", "ERS16387701", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.9171, 0.91541, 0.19718, 0.20005, 0.76759, 0.77285, 0.75547, 0.75357, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14897, "ERR12071833", "ERX11454458", "ERS16387700", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E114 3", "SAMEA114399008", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:114 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66709", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "114-3_S72_L007_R1_001.fastq.gz 114-3_S72_L007_R2_001.fastq.gz", "fastq fastq", 15510255012.0, 61548631.0, "ena RUN TAB 21 09 2023 13:32:15:294 66710", "0:126 1:126", "A:3024458012;C:4641826332;G:4764527525;T:3052903565;N:26539578", 126, 126, null, null, 3024458012, 4641826332, 4764527525, 3052903565, 26539578, "ERX11454458", "ERS16387700", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.85112, 0.84868, 0.17054, 0.17432, 0.79547, 0.79851, 0.73756, 0.8091, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14898, "ERR12071832", "ERX11454457", "ERS16387699", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E114 1", "SAMEA114399007", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:114 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66707", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "114-1_S27_L005_R1_001.fastq.gz 114-1_S27_L005_R2_001.fastq.gz", "fastq fastq", 15544755576.0, 61685538.0, "ena RUN TAB 21 09 2023 13:32:15:294 66708", "0:126 1:126", "A:3077913021;C:4638218386;G:4760672592;T:3065112184;N:2839393", 126, 126, null, null, 3077913021, 4638218386, 4760672592, 3065112184, 2839393, "ERX11454457", "ERS16387699", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.90822, 0.90777, 0.1775, 0.18112, 0.79263, 0.78808, 0.82214, 0.79489, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14899, "ERR12071831", "ERX11454456", "ERS16387698", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E113 9", "SAMEA114399006", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:113 9|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 9|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66705", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "113-9_S67_L006_R1_001.fastq.gz 113-9_S67_L006_R2_001.fastq.gz", "fastq fastq", 15414133644.0, 61167197.0, "ena RUN TAB 21 09 2023 13:32:15:293 66706", "0:126 1:126", "A:3185120611;C:4467167719;G:4606569127;T:3131094561;N:24181626", 126, 126, null, null, 3185120611, 4467167719, 4606569127, 3131094561, 24181626, "ERX11454456", "ERS16387698", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.94176, 0.94197, 0.17489, 0.17743, 0.76063, 0.76295, 0.75218, 0.75546, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14900, "ERR12071830", "ERX11454455", "ERS16387697", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E113 13", "SAMEA114399005", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:113 13|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 13|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66703", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "113-13_S71_L007_R1_001.fastq.gz 113-13_S71_L007_R2_001.fastq.gz", "fastq fastq", 18125498160.0, 71926580.0, "ena RUN TAB 21 09 2023 13:32:15:293 66704", "0:126 1:126", "A:3681246224;C:5316613237;G:5486708206;T:3609735923;N:31194570", 126, 126, null, null, 3681246224, 5316613237, 5486708206, 3609735923, 31194570, "ERX11454455", "ERS16387697", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.93952, 0.93814, 0.1717, 0.17395, 0.76627, 0.76976, 0.76533, 0.72702, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14901, "ERR12071829", "ERX11454454", "ERS16387696", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E113 11", "SAMEA114399004", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:113 11|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 11|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66701", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "113-11_S26_L005_R1_001.fastq.gz 113-11_S26_L005_R2_001.fastq.gz", "fastq fastq", 17918758872.0, 71106186.0, "ena RUN TAB 21 09 2023 13:32:15:293 66702", "0:126 1:126", "A:3460235614;C:5469489967;G:5622549540;T:3363214846;N:3268905", 126, 126, null, null, 3460235614, 5469489967, 5622549540, 3363214846, 3268905, "ERX11454454", "ERS16387696", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.94836, 0.94773, 0.16512, 0.16708, 0.79843, 0.79251, 0.79716, 0.79211, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14902, "ERR12071828", "ERX11454453", "ERS16387695", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E113 10", "SAMEA114399003", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:113 10|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 10|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66699", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "113-10_S75_L008_R1_001.fastq.gz 113-10_S75_L008_R2_001.fastq.gz", "fastq fastq", 22137738588.0, 87848169.0, "ena RUN TAB 21 09 2023 13:32:15:293 66700", "0:126 1:126", "A:4240961737;C:6714114283;G:6924397580;T:4216314997;N:41949991", 126, 126, null, null, 4240961737, 6714114283, 6924397580, 4216314997, 41949991, "ERX11454453", "ERS16387695", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.94101, 0.93949, 0.15969, 0.16256, 0.782, 0.78429, 0.78877, 0.78359, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14903, "ERR12071827", "ERX11454452", "ERS16387694", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E112 8", "SAMEA114399002", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:112 8|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:112 8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:292 66697", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "112-8_S74_L008_R1_001.fastq.gz 112-8_S74_L008_R2_001.fastq.gz", "fastq fastq", 15579825912.0, 61824706.0, "ena RUN TAB 21 09 2023 13:32:15:292 66698", "0:126 1:126", "A:3262384535;C:4470619467;G:4585527202;T:3231451715;N:29842993", 126, 126, null, null, 3262384535, 4470619467, 4585527202, 3231451715, 29842993, "ERX11454452", "ERS16387694", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.92603, 0.92484, 0.18249, 0.18589, 0.75917, 0.76335, 0.73196, 0.72728, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14904, "ERR12071826", "ERX11454451", "ERS16387693", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E112 7", "SAMEA114399001", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:112 7|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:112 7|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:292 66695", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "112-7_S66_L006_R1_001.fastq.gz 112-7_S66_L006_R2_001.fastq.gz", "fastq fastq", 20203529976.0, 80172738.0, "ena RUN TAB 21 09 2023 13:32:15:292 66696", "0:126 1:126", "A:4115948087;C:5902381830;G:6064166888;T:4089530757;N:31502414", 126, 126, null, null, 4115948087, 5902381830, 6064166888, 4089530757, 31502414, "ERX11454451", "ERS16387693", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.92896, 0.92845, 0.17083, 0.17434, 0.76146, 0.76337, 0.6945, 0.74323, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14905, "ERR12071825", "ERX11454450", "ERS16387692", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E112 5", "SAMEA114399000", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:112 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:112 5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:292 66693", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "112-5_S70_L007_R1_001.fastq.gz 112-5_S70_L007_R2_001.fastq.gz", "fastq fastq", 14979433392.0, 59442196.0, "ena RUN TAB 21 09 2023 13:32:15:292 66694", "0:126 1:126", "A:2989976300;C:4427492967;G:4545641644;T:2990769657;N:25552824", 126, 126, null, null, 2989976300, 4427492967, 4545641644, 2990769657, 25552824, "ERX11454450", "ERS16387692", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.9139, 0.91293, 0.18796, 0.1912, 0.78443, 0.78597, 0.79005, 0.77582, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14906, "ERR12071824", "ERX11454449", "ERS16387691", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "High stress", "E112 4", "SAMEA114398999", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:112 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:112 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:292 66691", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "112-4_S25_L005_R1_001.fastq.gz 112-4_S25_L005_R2_001.fastq.gz", "fastq fastq", 14850028368.0, 58928684.0, "ena RUN TAB 21 09 2023 13:32:15:292 66692", "0:126 1:126", "A:3108605429;C:4289376091;G:4392727411;T:3056545411;N:2774026", 126, 126, null, null, 3108605429, 4289376091, 4392727411, 3056545411, 2774026, "ERX11454449", "ERS16387691", "ERA27252154", "university of east anglia|European Nucleotide Archive", "university of east anglia", 2, 0.92451, 0.92555, 0.17853, 0.18265, 0.76501, 0.76106, 0.73074, 0.72504, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-09-21", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [14907, "ERR12071823", "ERX11454448", "ERS16387690", "ERP151293", "PRJEB66218", "Social stress in Zebrafish sperm", "b81525de-0f4f-4e41-8e34-f411e5590e7b", "Other", "Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", null, "Low stress", "E111 4", "SAMEA114398998", "University of East Anglia", "INSDC center name:University of East Anglia|Submitter Id:111 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:111 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq X paired end sequencing", "ena EXPERIMENT TAB 21 09 2023 13:32:15:291 66689", "125bp", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X", null, "ERP151293", "Illumina HiSeq X paired end sequencing", "ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21", "111-4_S8_L002_R1_001.fastq.gz 111-4_S8_L002_R2_001.fastq.gz", "fastq fastq", 17826911676.0, 70741713.0, "ena RUN TAB 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