{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Juvenile\" and tissue_curation_coarse = \"All anatomical structures\"", "rows": [[42301, "SRR5579865", "SRX2837982", "SRS2212147", "SRP107584", "PRJNA387320", "Danio rerio 1207 Raw sequence reads", "PRJNA387320", "Other", null, null, null, null, null, "1207 2", null, "breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "2002 2", "1207 2 S1 L001", "1207 2 S1 L001", "The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos  n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer\u0092s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP107584", null, null, null, null, 1531873131.0, 5203504.0, "1207 2 S2 L001 2 paired.fq.gz", "0:148.34 1:146.06", "A:384469512;C:380138079;G:381661689;T:385603823;N:28", 148, 146, null, null, 384469512, 380138079, 381661689, 385603823, 28, "SRX2837982", "SRS2212147", "SRA563090", "The Chinese University of Hong Kong|School of Life Sciences", "The Chinese University of Hong Kong", 2, 0.97313, 0.97391, 0.03931, 0.03966, 0.73675, 0.74186, 0.47243, 0.47819, 151, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2017-05-20", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [42302, "SRR5579866", "SRX2837981", "SRS2212146", "SRP107584", "PRJNA387320", "Danio rerio 1207 Raw sequence reads", "PRJNA387320", "Other", null, null, null, null, null, "1207 1", null, "breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "2002 1", "1207 1 S1 L001", "1207 1 S1 L001", "The embryos were subjected to RNA isolation. 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RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP107584", null, null, null, null, 1250178633.0, 4243308.0, "1207 1 S1 L001 2 paired.fq.gz", "0:148.83 1:145.79", "A:314820390;C:308887372;G:310674271;T:315796566;N:34", 148, 145, null, null, 314820390, 308887372, 310674271, 315796566, 34, "SRX2837981", "SRS2212146", "SRA563090", "The Chinese University of Hong Kong|School of Life Sciences", "The Chinese University of Hong Kong", 2, 0.97174, 0.9719, 0.04506, 0.04505, 0.73154, 0.73683, 0.4817, 0.48252, 150, 148, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2017-05-20", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [42303, "SRR5579867", "SRX2837980", "SRS2212145", "SRP107584", "PRJNA387320", "Danio rerio 1207 Raw sequence reads", "PRJNA387320", "Other", null, null, null, null, null, "AB 1", null, "breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT1", "AB1 S1 L001", "AB1 S1 L001", "The embryos were subjected to RNA isolation. 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RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP107584", null, null, null, null, 1045991851.0, 3554741.0, "1207 3 S3 L001 2 paired.fq.gz", "0:148.38 1:145.87", "A:263998819;C:257909132;G:259440555;T:264643331;N:14", 148, 145, null, null, 263998819, 257909132, 259440555, 264643331, 14, "SRX2837979", "SRS2212143", "SRA563090", "The Chinese University of Hong Kong|School of Life Sciences", "The Chinese University of Hong Kong", 2, 0.97252, 0.97273, 0.0409, 0.04037, 0.74213, 0.74574, 0.48248, 0.48634, 151, 151, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2017-05-20", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [42305, "SRR5579869", "SRX2837978", "SRS2212142", "SRP107584", "PRJNA387320", "Danio rerio 1207 Raw sequence reads", "PRJNA387320", "Other", null, null, null, null, null, "AB 3", null, "breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT3", "AB3 S1 L001", "AB3 S1 L001", "The embryos were subjected to RNA isolation. 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RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP107584", null, null, null, null, 1716453669.0, 5815815.0, "AB2 S2 L001 1 paired.fq.gz", "0:148.63 1:146.50", "A:430519895;C:426826400;G:426635292;T:432472082;N:0", 148, 146, null, null, 430519895, 426826400, 426635292, 432472082, 0, "SRX2837977", "SRS2212144", "SRA563090", "The Chinese University of Hong Kong|School of Life Sciences", "The Chinese University of Hong Kong", 2, 0.97735, 0.97725, 0.02854, 0.02833, 0.73196, 0.73484, 0.48256, 0.4861, 151, 151, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2017-05-20", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [42350, "SRR7410374", "SRX4281985", "SRS3446891", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. 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Postlethwait  University of Oregon|genotype:fancl nkhg10aEt  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 08", "30dpf fancl mutant 30 08", "30dpf fancl mutant 30 08", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151068", null, null, null, null, 5683582044.0, 22553897.0, "fancl mut 30 08 R1.fq.gz", "0:126 1:126", "A:1407291490;C:1395013891;G:1423770166;T:1456844244;N:662253", 126, 126, null, null, 1407291490, 1395013891, 1423770166, 1456844244, 662253, "SRX4281938", "SRS3446903", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.9455, 0.95135, 0.1075, 0.10757, 0.71912, 0.72196, 0.57287, 0.55078, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42398, "SRR7410422", "SRX4281937", "SRS3446903", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "fancl mutant 30dpf", "fancl mutant 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:fancl nkhg10aEt  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 01", "30dpf fancl mutant 30 01", "30dpf fancl mutant 30 01", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151068", null, null, null, null, 8917768188.0, 35387969.0, "fancl mut 30 01 R1.fq.gz", "0:126 1:126", "A:2184330162;C:2213012086;G:2262881514;T:2256511021;N:1033405", 126, 126, null, null, 2184330162, 2213012086, 2262881514, 2256511021, 1033405, "SRX4281937", "SRS3446903", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.95002, 0.95663, 0.11136, 0.11179, 0.72502, 0.72815, 0.57109, 0.54445, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42404, "SRR7410428", "SRX4281931", "SRS3446903", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "fancl mutant 30dpf", "fancl mutant 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:fancl nkhg10aEt  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 25", "30dpf fancl mutant 30 25", "30dpf fancl mutant 30 25", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151068", null, null, null, null, 10430314776.0, 41390138.0, "fancl mut 30 25 R1.fq.gz", "0:126 1:126", "A:2601755089;C:2535322569;G:2600718638;T:2691288565;N:1229915", 126, 126, null, null, 2601755089, 2535322569, 2600718638, 2691288565, 1229915, "SRX4281931", "SRS3446903", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.94533, 0.95212, 0.10271, 0.10301, 0.71549, 0.71823, 0.57327, 0.58016, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42405, "SRR7410429", "SRX4281930", "SRS3446903", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "fancl mutant 30dpf", "fancl mutant 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:fancl nkhg10aEt  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf fancl mutant sample 30 19", "30dpf fancl mutant 30 19", "30dpf fancl mutant 30 19", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151068", null, null, null, null, 5726761488.0, 22725244.0, "fancl mut 30 19 R2.fq.gz", "0:126 1:126", "A:1417828651;C:1399791137;G:1432389082;T:1476078215;N:674403", 126, 126, null, null, 1417828651, 1399791137, 1432389082, 1476078215, 674403, "SRX4281930", "SRS3446903", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.94187, 0.95012, 0.10759, 0.10798, 0.71944, 0.71928, 0.57165, 0.52896, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42416, "SRR7410440", "SRX4281919", "SRS3446900", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 wildtype 30dpf", "brca2 wildtype 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 27", "30dpf brca2 wild type 30 27", "30dpf brca2 wild type 30 27", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 10335588808.0, 34223804.0, "brca2 wt 30 27 TATGTGGC R2.fq.gz", "0:151 1:151", "A:2578068515;C:2550705556;G:2592943796;T:2612664094;N:1206847", 151, 151, null, null, 2578068515, 2550705556, 2592943796, 2612664094, 1206847, "SRX4281919", "SRS3446900", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.91509, 0.92944, 0.1198, 0.09246, 0.72794, 0.73476, 0.50295, 0.55616, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42417, "SRR7410441", "SRX4281918", "SRS3446900", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 wildtype 30dpf", "brca2 wildtype 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 19", "30dpf brca2 wild type 30 19", "30dpf brca2 wild type 30 19", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 16971362932.0, 56196566.0, "brca2 wt 30 19 TTCAGCTC R1.fq.gz", "0:151 1:151", "A:4261370563;C:4149954129;G:4237743108;T:4320302899;N:1992233", 151, 151, null, null, 4261370563, 4149954129, 4237743108, 4320302899, 1992233, "SRX4281918", "SRS3446900", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.90172, 0.92611, 0.10946, 0.08762, 0.71551, 0.71993, 0.50428, 0.59503, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42418, "SRR7410442", "SRX4281917", "SRS3446900", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 wildtype 30dpf", "brca2 wildtype 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 14", "30dpf brca2 wild type 30 14", "30dpf brca2 wild type 30 14", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 6864849882.0, 22731291.0, "brca2 wt 30 14 TTGCGTAC R2.fq.gz", "0:151 1:151", "A:1727616237;C:1676798537;G:1712647063;T:1746990291;N:797754", 151, 151, null, null, 1727616237, 1676798537, 1712647063, 1746990291, 797754, "SRX4281917", "SRS3446900", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.92049, 0.93514, 0.11, 0.08759, 0.73511, 0.74349, 0.51728, 0.58993, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42420, "SRR7410444", "SRX4281915", "SRS3446900", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 wildtype 30dpf", "brca2 wildtype 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 17", "30dpf brca2 wild type 30 17", "30dpf brca2 wild type 30 17", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 8432584732.0, 27922466.0, "brca2 wt 30 17 TGCGTGAA R2.fq.gz", "0:151 1:151", "A:2132479978;C:2035633473;G:2088942653;T:2174550395;N:978233", 151, 151, null, null, 2132479978, 2035633473, 2088942653, 2174550395, 978233, "SRX4281915", "SRS3446900", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.91011, 0.9287, 0.1076, 0.08793, 0.70627, 0.71431, 0.49536, 0.58516, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42421, "SRR7410445", "SRX4281914", "SRS3446900", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 wildtype 30dpf", "brca2 wildtype 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434 +/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 wild type sample 30 16", "30dpf brca2 wild type 30 16", "30dpf brca2 wild type 30 16", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 5787544912.0, 19164056.0, "brca2 wt 30 16 TTGACTCT R1.fq.gz", "0:151 1:151", "A:1470953427;C:1394911620;G:1427129077;T:1493879392;N:671396", 151, 151, null, null, 1470953427, 1394911620, 1427129077, 1493879392, 671396, "SRX4281914", "SRS3446900", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.90129, 0.91879, 0.11795, 0.09608, 0.69909, 0.70818, 0.49724, 0.5781, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42441, "SRR7410465", "SRX4281894", "SRS3446892", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 mutant 30dpf", "brca2 mutant 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 13", "30dpf brca2 mutant 30 13", "30dpf brca2 mutant 30 13", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 7614746082.0, 25214391.0, "brca2 mut 30 13 GTGTCCTT R2.fq.gz", "0:151 1:151", "A:1953796672;C:1825224132;G:1858553376;T:1976291422;N:880480", 151, 151, null, null, 1953796672, 1825224132, 1858553376, 1976291422, 880480, "SRX4281894", "SRS3446892", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.90472, 0.92046, 0.1248, 0.1051, 0.69836, 0.70745, 0.43736, 0.58121, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42442, "SRR7410466", "SRX4281893", "SRS3446892", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 mutant 30dpf", "brca2 mutant 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 12", "30dpf brca2 mutant 30 12", "30dpf brca2 mutant 30 12", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 6609294160.0, 21885080.0, "brca2 mut 30 12 TGTTCTCC R1.fq.gz", "0:151 1:151", "A:1663996252;C:1611724064;G:1649391730;T:1683416159;N:765955", 151, 151, null, null, 1663996252, 1611724064, 1649391730, 1683416159, 765955, "SRX4281893", "SRS3446892", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.92261, 0.93707, 0.12282, 0.10062, 0.72555, 0.73655, 0.50213, 0.55978, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42443, "SRR7410467", "SRX4281892", "SRS3446892", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 mutant 30dpf", "brca2 mutant 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 11", "30dpf brca2 mutant 30 11", "30dpf brca2 mutant 30 11", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 3609770062.0, 11952881.0, "brca2 mut 30 11 ATCACGTT R2.fq.gz", "0:151 1:151", "A:910534494;C:877404076;G:898143524;T:923267603;N:420365", 151, 151, null, null, 910534494, 877404076, 898143524, 923267603, 420365, "SRX4281892", "SRS3446892", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.90353, 0.92062, 0.11856, 0.09432, 0.72809, 0.73669, 0.44186, 0.57479, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42447, "SRR7410471", "SRX4281888", "SRS3446892", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 mutant 30dpf", "brca2 mutant 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 36", "30dpf brca2 mutant 30 36", "30dpf brca2 mutant 30 36", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 6899944698.0, 22847499.0, "brca2 mut 30 36 GAGGTGCT R1.fq.gz", "0:151 1:151", "A:1745582542;C:1669300984;G:1707455172;T:1776814198;N:791802", 151, 151, null, null, 1745582542, 1669300984, 1707455172, 1776814198, 791802, "SRX4281888", "SRS3446892", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.91438, 0.93255, 0.11037, 0.09276, 0.72088, 0.73024, 0.50255, 0.57014, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42448, "SRR7410472", "SRX4281887", "SRS3446892", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "brca2 mutant 30dpf", "brca2 mutant 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:brca2 ZM 00057434  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf brca2 mutant sample 30 18", "30dpf brca2 mutant 30 18", "30dpf brca2 mutant 30 18", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP151068", null, null, null, null, 9162516316.0, 30339458.0, "brca2 mut 30 18 GTAAGGTG R2.fq.gz", "0:151 1:151", "A:2312465867;C:2223181568;G:2268715689;T:2357087788;N:1065404", 151, 151, null, null, 2312465867, 2223181568, 2268715689, 2357087788, 1065404, "SRX4281887", "SRS3446892", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.91218, 0.93164, 0.10691, 0.08773, 0.73464, 0.74306, 0.50561, 0.58578, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [42450, "SRR7410474", "SRX4281885", "SRS3446891", "SRP151068", "PRJNA387484", "RNA Seq of a Zebrafish Fanconi Mutant", "PRJNA387484", "Transcriptome Analysis", "We conducted RNA seq analysis of zebrafish fancl mutants and wild type siblings at 4dpf  10dpf  14dpf  18dpf  22dpf  26dpf  and 30dpf. RNA was extracted from the whole organism and libraries were prepared with the BIOO NEXTflex Rapid Directional qRNA Seq Kit.", null, null, "RNA seq library", "fancl wildtype 30dpf", "fancl wildtype 30dpf", null, "strain:AB|age:30 dpf|sex:not applicable|tissue:whole organism|biomaterial provider:John H. Postlethwait  University of Oregon|genotype:fancl nkhg10aEt +/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 30dpf fancl wild type sample 30 30", "30dpf fancl wild type 30 30", "30dpf fancl wild type 30 30", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP151068", null, null, null, null, 10131111648.0, 40202824.0, "fancl wt 30 30 R1.fq.gz", "0:126 1:126", "A:2542923952;C:2446585748;G:2508652587;T:2631768070;N:1181291", 126, 126, null, null, 2542923952, 2446585748, 2508652587, 2631768070, 1181291, "SRX4281885", "SRS3446891", "SRA726408", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.94391, 0.95296, 0.107, 0.10797, 0.72786, 0.73115, 0.58931, 0.57476, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-21", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54727, "SRR10150436", "SRX6875873", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I4S2", "I4S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I4-Hiseq_S2_L001_R1_001.fastq.gz S3-I4-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 3487596300.0, 11625321.0, "S3 I4 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:892777135;C:554604922;G:602698080;T:1437353489;N:162674", 150, 150, null, null, 892777135, 554604922, 602698080, 1437353489, 162674, "SRX6875873", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.20171, 0.89797, 0.05294, 0.15018, 0.98557, 0.78865, 0.5155, 0.57581, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54728, "SRR10150437", "SRX6875872", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I4S1", "I4S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I4-Hiseq_S1_L001_R1_001.fastq.gz S3-I4-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 7508763300.0, 25029211.0, "S3 I4 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:1913388616;C:1347525105;G:1432782100;T:2815014523;N:52956", 150, 150, null, null, 1913388616, 1347525105, 1432782100, 2815014523, 52956, "SRX6875872", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.07221, 0.85601, 0.01751, 0.14578, 0.98569, 0.78642, 0.49143, 0.56028, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54729, "SRR10150438", "SRX6875871", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I3S2", "I3S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I3-Hiseq_S2_L001_R1_001.fastq.gz S3-I3-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 4273728900.0, 14245763.0, "S3 I3 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:1093044190;C:680068409;G:740119940;T:1760292389;N:203972", 150, 150, null, null, 1093044190, 680068409, 740119940, 1760292389, 203972, "SRX6875871", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.20465, 0.90036, 0.05289, 0.14865, 0.98553, 0.7877, 0.49162, 0.55234, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54730, "SRR10150439", "SRX6875870", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I3S1", "I3S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I3-Hiseq_S1_L001_R1_001.fastq.gz S3-I3-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 9027772200.0, 30092574.0, "S3 I3 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:2295058606;C:1618993604;G:1725968569;T:3387689160;N:62261", 150, 150, null, null, 2295058606, 1618993604, 1725968569, 3387689160, 62261, "SRX6875870", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.07429, 0.86204, 0.01816, 0.14367, 0.98638, 0.78754, 0.51152, 0.56418, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54731, "SRR10150440", "SRX6875869", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I2S2", "I2S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I2-Hiseq_S2_L001_R1_001.fastq.gz S3-I2-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 3198554400.0, 10661848.0, "S3 I2 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:818748615;C:508568675;G:554517575;T:1316569216;N:150319", 150, 150, null, null, 818748615, 508568675, 554517575, 1316569216, 150319, "SRX6875869", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.2074, 0.89961, 0.05315, 0.14953, 0.98514, 0.78849, 0.48568, 0.56678, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54732, "SRR10150441", "SRX6875868", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I2S1", "I2S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I2-Hiseq_S1_L001_R1_001.fastq.gz S3-I2-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 7025021100.0, 23416737.0, "S3 I2 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:1791257403;C:1265471598;G:1350119282;T:2618125524;N:47293", 150, 150, null, null, 1791257403, 1265471598, 1350119282, 2618125524, 47293, "SRX6875868", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.0595, 0.8397, 0.01378, 0.14017, 0.98602, 0.78618, 0.49684, 0.57243, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54733, "SRR10150442", "SRX6875867", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I1S2", "I1S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I1-Hiseq_S2_L001_R1_001.fastq.gz S3-I1-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 3657667800.0, 12192226.0, "S3 I1 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:936855915;C:580324428;G:630608753;T:1509707910;N:170794", 150, 150, null, null, 936855915, 580324428, 630608753, 1509707910, 170794, "SRX6875867", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.20478, 0.89817, 0.05194, 0.15048, 0.98543, 0.78817, 0.49956, 0.57664, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54734, "SRR10150443", "SRX6875866", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I1S1", "I1S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I1-Hiseq_S1_L001_R1_001.fastq.gz S3-I1-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 7809763800.0, 26032546.0, "S3 I1 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:1991021603;C:1400155384;G:1489635110;T:2928896892;N:54811", 150, 150, null, null, 1991021603, 1400155384, 1489635110, 2928896892, 54811, "SRX6875866", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.06891, 0.85095, 0.01881, 0.14251, 0.98555, 0.78772, 0.49154, 0.57233, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59140, "SRR11684023", "SRX8244826", "SRS6592463", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf csf1rdm 3", "GSM4512715", null, "tissue:whole fish|developmental stage:33 dpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf csf1rdm 3", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512715", "GSM4512715: 33dpf csf1rdm 3; Danio rerio; RNA Seq", "GSM4512715", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512715", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_csf1rdm_3_R2.fastq.gz 33dpf_csf1rdm_3_R1.fastq.gz", "fastq fastq", 4266500984.0, 21121292.0, "GSM4512715 r1", "0:101 1:101", "A:1228176589;C:888764172;G:911251380;T:1238297282;N:11561", 101, 101, null, null, 1228176589, 888764172, 911251380, 1238297282, 11561, "SRX8244826", "SRS6592463", "SRA1072140", "GEO", "Erasmus MC", 2, 0.90846, 0.8852, 0.18604, 0.18551, 0.77149, 0.78056, 0.47511, 0.46363, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59141, "SRR11684022", "SRX8244825", "SRS6592462", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf csf1rdm 2", "GSM4512714", null, "tissue:whole fish|developmental stage:33 dpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf csf1rdm 2", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512714", "GSM4512714: 33dpf csf1rdm 2; Danio rerio; RNA Seq", "GSM4512714", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512714", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_csf1rdm_2_R2.fastq.gz 33dpf_csf1rdm_2_R1.fastq.gz", "fastq fastq", 34856013646.0, 172554523.0, "GSM4512714 r1", "0:101 1:101", "A:10025368414;C:7294167881;G:7483951837;T:10052430673;N:94841", 101, 101, null, null, 10025368414, 7294167881, 7483951837, 10052430673, 94841, "SRX8244825", "SRS6592462", "SRA1072140", "GEO", "Erasmus MC", 2, 0.90986, 0.88677, 0.1819, 0.18005, 0.7601, 0.76921, 0.48551, 0.47188, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59142, "SRR11684021", "SRX8244824", "SRS6592461", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf csf1rdm 1", "GSM4512713", null, "tissue:whole fish|developmental stage:33 dpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf csf1rdm 1", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512713", "GSM4512713: 33dpf csf1rdm 1; Danio rerio; RNA Seq", "GSM4512713", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512713", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_csf1rdm_1_R1.fastq.gz 33dpf_csf1rdm_1_R2.fastq.gz", "fastq fastq", 3251371598.0, 16095899.0, "GSM4512713 r1", "0:101 1:101", "A:938620484;C:677648040;G:693531098;T:941563341;N:8635", 101, 101, null, null, 938620484, 677648040, 693531098, 941563341, 8635, "SRX8244824", "SRS6592461", "SRA1072140", "GEO", "Erasmus MC", 2, 0.90369, 0.88203, 0.18089, 0.17771, 0.78234, 0.78847, 0.47498, 0.47606, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59143, "SRR11684020", "SRX8244823", "SRS6592460", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf control 3", "GSM4512712", null, "tissue:whole fish|developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf control 3", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512712", "GSM4512712: 33dpf control 3; Danio rerio; RNA Seq", "GSM4512712", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512712", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_control_3_R1.fastq.gz 33dpf_control_3_R2.fastq.gz", "fastq fastq", 2712847880.0, 13429940.0, "GSM4512712 r1", "0:101 1:101", "A:772539767;C:566195541;G:587191020;T:786914116;N:7436", 101, 101, null, null, 772539767, 566195541, 587191020, 786914116, 7436, "SRX8244823", "SRS6592460", "SRA1072140", "GEO", "Erasmus MC", 2, 0.93009, 0.89728, 0.17089, 0.17058, 0.74548, 0.75722, 0.48148, 0.47178, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59144, "SRR11684019", "SRX8244822", "SRS6592459", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf control 2", "GSM4512711", null, "tissue:whole fish|developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf control 2", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512711", "GSM4512711: 33dpf control 2; Danio rerio; RNA Seq", "GSM4512711", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512711", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_control_2_R2.fastq.gz 33dpf_control_2_R1.fastq.gz", "fastq fastq", 1740822264.0, 8617932.0, "GSM4512711 r1", "0:101 1:101", "A:496913292;C:363966331;G:377438086;T:502499900;N:4655", 101, 101, null, null, 496913292, 363966331, 377438086, 502499900, 4655, "SRX8244822", "SRS6592459", "SRA1072140", "GEO", "Erasmus MC", 2, 0.92011, 0.89184, 0.16484, 0.16269, 0.7541, 0.7655, 0.47531, 0.46847, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59145, "SRR11684018", "SRX8244821", "SRS6592458", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf control 1", "GSM4512710", null, "tissue:whole fish|developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf control 1", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512710", "GSM4512710: 33dpf control 1; Danio rerio; RNA Seq", "GSM4512710", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512710", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_control_1_R2.fastq.gz 33dpf_control_1_R1.fastq.gz", "fastq fastq", 3546165954.0, 17555277.0, "GSM4512710 r1", "0:101 1:101", "A:1004040828;C:754797131;G:787411451;T:999907224;N:9320", 101, 101, null, null, 1004040828, 754797131, 787411451, 999907224, 9320, "SRX8244821", "SRS6592458", "SRA1072140", "GEO", "Erasmus MC", 2, 0.93722, 0.91292, 0.14991, 0.14981, 0.75191, 0.76171, 0.47117, 0.46955, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68196, "SRR17658725", "SRX13826756", "SRS11705914", "SRP355720", "PRJNA798511", "Comparative analysis of 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Science and Technology", 2, 0.93932, 0.94095, 0.06489, 0.06559, 0.77871, 0.77759, 0.56384, 0.56447, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68200, "SRR17658729", "SRX13826752", "SRS11705910", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C45d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:45dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C45D", "C45D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20413229700.0, 68044099.0, "C45D.7z", "0:150 1:150", "A:5619395833;C:4581611789;G:4543973618;T:5667873613;N:374847", 150, 150, null, null, 5619395833, 4581611789, 4543973618, 5667873613, 374847, "SRX13826752", "SRS11705910", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.86848, 0.87064, 0.0719, 0.07252, 0.69879, 0.69834, 0.52279, 0.51074, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68201, "SRR17658730", "SRX13826751", "SRS11705909", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C35d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:35dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C35D", "C35D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20469803700.0, 68232679.0, "C35D.7z", "0:150 1:150", "A:5556774511;C:4678377106;G:4627472920;T:5606765895;N:413268", 150, 150, null, null, 5556774511, 4678377106, 4627472920, 5606765895, 413268, "SRX13826751", "SRS11705909", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.93663, 0.93871, 0.06853, 0.06895, 0.6982, 0.69901, 0.51209, 0.51148, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69610, "SRR18959644", "SRX15036823", "SRS12783659", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 3", "GSM6070558", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070558", "GSM6070558: T60d 3; Danio rerio; RNA Seq", "GSM6070558 r1", "GSM6070558", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_3_1.fq.gz T60d_3_2.fq.gz", "fastq fastq", 6668586300.0, 44457242.0, "GSM6070558 r1", "0:150 1:150", "A:1798105768;C:1533776293;G:1519933345;T:1816635529;N:135365", 150, 150, null, null, 1798105768, 1533776293, 1519933345, 1816635529, 135365, "SRX15036823", "SRS12783659", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94696, null, 0.03818, null, 0.72754, null, 0.44424, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69611, "SRR18959645", "SRX15036822", "SRS12783660", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 2", "GSM6070557", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070557", "GSM6070557: T60d 2; Danio rerio; RNA Seq", "GSM6070557 r1", "GSM6070557", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_2_1.fq.gz T60d_2_2.fq.gz", "fastq fastq", 6790474800.0, 45269832.0, "GSM6070557 r1", "0:150 1:150", "A:1792022273;C:1601949824;G:1583360851;T:1813022005;N:119847", 150, 150, null, null, 1792022273, 1601949824, 1583360851, 1813022005, 119847, "SRX15036822", "SRS12783660", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9518, null, 0.03662, null, 0.72892, null, 0.50564, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69612, "SRR18959646", "SRX15036821", "SRS12783661", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 1", "GSM6070556", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070556", "GSM6070556: T60d 1; Danio rerio; RNA Seq", "GSM6070556 r1", "GSM6070556", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_1_1.fq.gz T60d_1_2.fq.gz", "fastq fastq", 6875681100.0, 45837874.0, "GSM6070556 r1", "0:150 1:150", "A:1892073166;C:1547272647;G:1532480808;T:1903720960;N:133519", 150, 150, null, null, 1892073166, 1547272647, 1532480808, 1903720960, 133519, "SRX15036821", "SRS12783661", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93516, null, 0.0737, null, 0.70394, null, 0.55661, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69613, "SRR18959647", "SRX15036820", "SRS12783658", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 3", "GSM6070555", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070555", "GSM6070555: T45d 3; Danio rerio; RNA Seq", "GSM6070555 r1", "GSM6070555", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_3_1.fq.gz T45d_3_2.fq.gz", "fastq fastq", 6677602800.0, 44517352.0, "GSM6070555 r1", "0:150 1:150", "A:1776927020;C:1564627916;G:1551750199;T:1784113081;N:184584", 150, 150, null, null, 1776927020, 1564627916, 1551750199, 1784113081, 184584, "SRX15036820", "SRS12783658", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.95333, null, 0.04626, null, 0.79788, null, 0.53869, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69614, "SRR18959648", "SRX15036819", "SRS12783657", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 2", "GSM6070554", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070554", "GSM6070554: T45d 2; Danio rerio; RNA Seq", "GSM6070554 r1", "GSM6070554", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_2_1.fq.gz T45d_2_2.fq.gz", "fastq fastq", 6866885100.0, 45779234.0, "GSM6070554 r1", "0:150 1:150", "A:1855996561;C:1572989256;G:1559095064;T:1878636946;N:167273", 150, 150, null, null, 1855996561, 1572989256, 1559095064, 1878636946, 167273, "SRX15036819", "SRS12783657", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.85691, null, 0.0428, null, 0.70059, null, 0.48517, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69615, "SRR18959649", "SRX15036818", "SRS12783655", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 1", "GSM6070553", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070553", "GSM6070553: T45d 1; Danio rerio; RNA Seq", "GSM6070553 r1", "GSM6070553", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_1_1.fq.gz T45d_1_2.fq.gz", "fastq fastq", 6686072400.0, 44573816.0, "GSM6070553 r1", "0:150 1:150", "A:1811892628;C:1525390412;G:1521098470;T:1827658727;N:32163", 150, 150, null, null, 1811892628, 1525390412, 1521098470, 1827658727, 32163, "SRX15036818", "SRS12783655", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.83063, null, 0.04482, null, 0.75227, null, 0.53268, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69616, "SRR18959650", "SRX15036817", "SRS12783656", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 3", "GSM6070552", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070552", "GSM6070552: T35d 3; Danio rerio; RNA Seq", "GSM6070552 r1", "GSM6070552", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_3_1.fq.gz T35d_3_2.fq.gz", "fastq fastq", 6886247700.0, 45908318.0, "GSM6070552 r1", "0:150 1:150", "A:1822190170;C:1616493163;G:1597658988;T:1849741504;N:163875", 150, 150, null, null, 1822190170, 1616493163, 1597658988, 1849741504, 163875, "SRX15036817", "SRS12783656", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94299, null, 0.03719, null, 0.71165, null, 0.49413, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69617, "SRR18959651", "SRX15036816", "SRS12783654", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 2", "GSM6070551", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070551", "GSM6070551: T35d 2; Danio rerio; RNA Seq", "GSM6070551 r1", "GSM6070551", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_2_1.fq.gz T35d_2_2.fq.gz", "fastq fastq", 6851241900.0, 45674946.0, "GSM6070551 r1", "0:150 1:150", "A:1925245234;C:1503184374;G:1483632128;T:1939009289;N:170875", 150, 150, null, null, 1925245234, 1503184374, 1483632128, 1939009289, 170875, "SRX15036816", "SRS12783654", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.86703, null, 0.08277, null, 0.70619, null, 0.47871, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69618, "SRR18959652", "SRX15036815", "SRS12783653", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 1", "GSM6070550", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070550", "GSM6070550: T35d 1; Danio rerio; RNA Seq", "GSM6070550 r1", "GSM6070550", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_1_1.fq.gz T35d_1_2.fq.gz", "fastq fastq", 6893013600.0, 45953424.0, "GSM6070550 r1", "0:150 1:150", "A:1913222428;C:1535252220;G:1516792188;T:1927599483;N:147281", 150, 150, null, null, 1913222428, 1535252220, 1516792188, 1927599483, 147281, "SRX15036815", "SRS12783653", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93126, null, 0.08861, null, 0.70711, null, 0.53182, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69619, "SRR18959653", "SRX15036814", "SRS12783652", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 3", "GSM6070549", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070549", "GSM6070549: C60d 3; Danio rerio; RNA Seq", "GSM6070549 r1", "GSM6070549", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_3_1.fq.gz C60d_3_2.fq.gz", "fastq fastq", 6732458700.0, 44883058.0, "GSM6070549 r1", "0:150 1:150", "A:1840891044;C:1527037740;G:1515664962;T:1848770869;N:94085", 150, 150, null, null, 1840891044, 1527037740, 1515664962, 1848770869, 94085, "SRX15036814", "SRS12783652", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94478, null, 0.05996, null, 0.73661, null, 0.56885, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69620, "SRR18959654", "SRX15036813", "SRS12783651", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 2", "GSM6070548", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070548", "GSM6070548: C60d 2; Danio rerio; RNA Seq", "GSM6070548 r1", "GSM6070548", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_2_1.fq.gz C60d_2_2.fq.gz", "fastq fastq", 6920478600.0, 46136524.0, "GSM6070548 r1", "0:150 1:150", "A:1860288879;C:1602876302;G:1589399217;T:1867783032;N:131170", 150, 150, null, null, 1860288879, 1602876302, 1589399217, 1867783032, 131170, "SRX15036813", "SRS12783651", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.95235, null, 0.05236, null, 0.74836, null, 0.55427, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69621, "SRR18959655", "SRX15036812", "SRS12783650", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 1", "GSM6070547", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070547", "GSM6070547: C60d 1; Danio rerio; RNA Seq", "GSM6070547 r1", "GSM6070547", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_1_1.fq.gz C60d_1_2.fq.gz", "fastq fastq", 6744639300.0, 44964262.0, "GSM6070547 r1", "0:150 1:150", "A:1855599360;C:1516548729;G:1501772747;T:1870587619;N:130845", 150, 150, null, null, 1855599360, 1516548729, 1501772747, 1870587619, 130845, "SRX15036812", "SRS12783650", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93949, null, 0.06857, null, 0.73805, null, 0.54443, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69622, "SRR18959656", "SRX15036811", "SRS12783649", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 3", "GSM6070546", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070546", "GSM6070546: C45d 3; Danio rerio; RNA Seq", "GSM6070546 r1", "GSM6070546", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_3_1.fq.gz C45d_3_2.fq.gz", "fastq fastq", 6743568300.0, 44957122.0, "GSM6070546 r1", "0:150 1:150", "A:1852733188;C:1516814321;G:1505754587;T:1868137549;N:128655", 150, 150, null, null, 1852733188, 1516814321, 1505754587, 1868137549, 128655, "SRX15036811", "SRS12783649", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.87046, null, 0.07264, null, 0.69996, null, 0.51275, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69623, "SRR18959657", "SRX15036810", "SRS12783648", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 2", "GSM6070545", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070545", "GSM6070545: C45d 2; Danio rerio; RNA Seq", "GSM6070545 r1", "GSM6070545", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_2_1.fq.gz C45d_2_2.fq.gz", "fastq fastq", 6742016100.0, 44946774.0, "GSM6070545 r1", "0:150 1:150", "A:1859613225;C:1508260261;G:1496299109;T:1877718155;N:125350", 150, 150, null, null, 1859613225, 1508260261, 1496299109, 1877718155, 125350, "SRX15036810", "SRS12783648", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.84381, null, 0.07253, null, 0.68769, null, 0.51224, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69624, "SRR18959658", "SRX15036809", "SRS12783647", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 1", "GSM6070544", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070544", "GSM6070544: C45d 1; Danio rerio; RNA Seq", "GSM6070544 r1", "GSM6070544", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_1_1.fq.gz C45d_1_2.fq.gz", "fastq fastq", 6927645300.0, 46184302.0, "GSM6070544 r1", "0:150 1:150", "A:1907049420;C:1556537207;G:1541919922;T:1922017909;N:120842", 150, 150, null, null, 1907049420, 1556537207, 1541919922, 1922017909, 120842, "SRX15036809", "SRS12783647", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.89529, null, 0.07244, null, 0.71703, null, 0.53737, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69625, "SRR18959659", "SRX15036808", "SRS12783646", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 3", "GSM6070543", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070543", "GSM6070543: C35d 3; Danio rerio; RNA Seq", "GSM6070543 r1", "GSM6070543", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_3_1.fq.gz C35d_3_2.fq.gz", "fastq fastq", 6874832400.0, 45832216.0, "GSM6070543 r1", "0:150 1:150", "A:1849406781;C:1586828671;G:1570455371;T:1867999362;N:142215", 150, 150, null, null, 1849406781, 1586828671, 1570455371, 1867999362, 142215, "SRX15036808", "SRS12783646", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94372, null, 0.06412, null, 0.71043, null, 0.5035, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69626, "SRR18959660", "SRX15036807", "SRS12783645", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 2", "GSM6070542", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070542", "GSM6070542: C35d 2; Danio rerio; RNA Seq", "GSM6070542 r1", "GSM6070542", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_2_1.fq.gz C35d_2_2.fq.gz", "fastq fastq", 6709504200.0, 44730028.0, "GSM6070542 r1", "0:150 1:150", "A:1832012065;C:1521825928;G:1505192413;T:1850347840;N:125954", 150, 150, null, null, 1832012065, 1521825928, 1505192413, 1850347840, 125954, "SRX15036807", "SRS12783645", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9254, null, 0.07577, null, 0.67537, null, 0.51805, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69627, "SRR18959661", "SRX15036806", "SRS12783644", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 1", "GSM6070541", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070541", "GSM6070541: C35d 1; Danio rerio; RNA Seq", "GSM6070541 r1", "GSM6070541", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_1_1.fq.gz C35d_1_2.fq.gz", "fastq fastq", 6885467100.0, 45903114.0, "GSM6070541 r1", "0:150 1:150", "A:1875355665;C:1569722507;G:1551825136;T:1888418693;N:145099", 150, 150, null, null, 1875355665, 1569722507, 1551825136, 1888418693, 145099, "SRX15036806", "SRS12783644", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9444, 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"A:1737437159;C:1534810355;G:1561501860;T:1726789854;N:10622", 151, 151, null, null, 1737437159, 1534810355, 1561501860, 1726789854, 10622, "SRX15447454", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93435, 0.93393, 0.06267, 0.06345, 0.65776, 0.65871, 0.49762, 0.49344, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70057, "SRR19392695", "SRX15447453", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "mut 2 45dpf", "mut 2 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "6Hmut_2_R1.fastq.gz 6Hmut_2_R2.fastq.gz", "fastq fastq", 6478614532.0, 21452366.0, "6Hmut 2 R1.fastq.gz", "0:151 1:151", "A:1722746415;C:1511301958;G:1537581513;T:1706974238;N:10408", 151, 151, null, null, 1722746415, 1511301958, 1537581513, 1706974238, 10408, "SRX15447453", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.94033, 0.93884, 0.0793, 0.07897, 0.66979, 0.67063, 0.51091, 0.50721, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70058, "SRR19392696", "SRX15447452", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "mut 1 45dpf", "mut 1 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "6Hmut_1_R1.fastq.gz 6Hmut_1_R2.fastq.gz", "fastq fastq", 7131696780.0, 23614890.0, "6Hmut 1 R1.fastq.gz", "0:151 1:151", "A:1896556650;C:1662708805;G:1692110221;T:1880309012;N:12092", 151, 151, null, null, 1896556650, 1662708805, 1692110221, 1880309012, 12092, "SRX15447452", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93784, 0.93841, 0.07685, 0.07715, 0.65969, 0.65999, 0.50615, 0.51174, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70059, "SRR19392697", "SRX15447451", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "wt 3 45dpf", "wt 3 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "wt_3_R1.fastq.gz wt_3_R2.fastq.gz", "fastq fastq", 6772530000.0, 22575100.0, "wt 3 R1.fastq.gz", "0:150 1:150", "A:1761127291;C:1612285256;G:1643602723;T:1755489964;N:24766", 150, 150, null, null, 1761127291, 1612285256, 1643602723, 1755489964, 24766, "SRX15447451", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.94155, 0.94016, 0.04781, 0.04747, 0.67054, 0.67227, 0.49488, 0.49322, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70060, "SRR19392698", "SRX15447450", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "wt 2 45dpf", "wt 2 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "wt_2_R1.fastq.gz wt_2_R2.fastq.gz", "fastq fastq", 7643857500.0, 25479525.0, "wt 2 R1.fastq.gz", "0:150 1:150", "A:1983773833;C:1824285264;G:1856615811;T:1979155020;N:27572", 150, 150, null, null, 1983773833, 1824285264, 1856615811, 1979155020, 27572, "SRX15447450", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93966, 0.93936, 0.04464, 0.04509, 0.66947, 0.67006, 0.47294, 0.48847, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70061, "SRR19392699", "SRX15447449", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "wt 1 45dpf", "wt 1 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "wt_1_R1.fastq.gz wt_1_R2.fastq.gz", "fastq fastq", 7810923300.0, 26036411.0, "wt 1 R1.fastq.gz", "0:150 1:150", "A:2023252187;C:1867703140;G:1901935578;T:2018003438;N:28957", 150, 150, null, null, 2023252187, 1867703140, 1901935578, 2018003438, 28957, "SRX15447449", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.94254, 0.94222, 0.04298, 0.04298, 0.66884, 0.67073, 0.47763, 0.48746, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72671, "SRR23060055", "SRX19013379", "SRS16433016", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "BPA225 3", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z908", "Z908", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "BPA225_3_Clean_Data1.fq.gz BPA225_3_Clean_Data2.fq.gz", "fastq fastq", 5922430705.0, 21094865.0, "BPA225 3 Clean Data1.fq.gz", null, null, null, null, null, null, null, null, null, null, null, "SRX19013379", "SRS16433016", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.94064, 0.94209, 0.10366, 0.10189, 0.70092, 0.6997, 0.46735, 0.4612, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72672, "SRR23060056", "SRX19013378", "SRS16433015", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "BPA225 2", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z907", "Z907", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "BPA225_2_Clean_Data1.fq.gz BPA225_2_Clean_Data2.fq.gz", "fastq fastq", 5509331897.0, 19639714.0, "BPA225 2 Clean Data1.fq.gz", null, null, null, null, null, null, null, null, null, null, null, "SRX19013378", "SRS16433015", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.9374, 0.93862, 0.11618, 0.11425, 0.69972, 0.69952, 0.46205, 0.46585, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72673, "SRR23060057", "SRX19013377", "SRS16433014", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "BPA225 1", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z906", "Z906", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "BPA225_1_Clean_Data1.fq.gz BPA225_1_Clean_Data2.fq.gz", "fastq fastq", 6015141019.0, 21413611.0, "BPA225 1 Clean Data1.fq.gz", "0:140.46 1:140.44", "A:1623319583;C:1384519528;G:1394796849;T:1612405771;N:99288", 140, 140, null, null, 1623319583, 1384519528, 1394796849, 1612405771, 99288, "SRX19013377", "SRS16433014", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.9392, 0.94002, 0.10822, 0.10578, 0.69146, 0.69063, 0.46651, 0.4618, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72674, "SRR23060058", "SRX19013376", "SRS16433013", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "BPA15 3", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z905", "Z905", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "BPA15_3_Clean_Data1.fq.gz BPA15_3_Clean_Data2.fq.gz", "fastq fastq", 5412693513.0, 19255194.0, "BPA15 3 Clean Data1.fq.gz", null, null, null, null, null, null, null, null, null, null, null, "SRX19013376", "SRS16433013", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.939, 0.93943, 0.11111, 0.10838, 0.69798, 0.69777, 0.46519, 0.46877, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72675, "SRR23060059", "SRX19013375", "SRS16433012", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "BPA15 2", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z904", "Z904", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "BPA15_2_Clean_Data1.fq.gz BPA15_2_Clean_Data2.fq.gz", "fastq fastq", 5836868617.0, 20778949.0, "BPA15 2 Clean Data1.fq.gz", "0:140.46 1:140.45", "A:1603966024;C:1315242512;G:1325577058;T:1591978988;N:104035", 140, 140, null, null, 1603966024, 1315242512, 1325577058, 1591978988, 104035, "SRX19013375", "SRS16433012", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.93522, 0.93486, 0.12945, 0.12692, 0.69735, 0.69702, 0.47307, 0.47198, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72676, "SRR23060060", "SRX19013374", "SRS16433010", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "BPA15 1", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z903", "Z903", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "BPA15_1_Clean_Data1.fq.gz BPA15_1_Clean_Data2.fq.gz", "fastq fastq", 5565976271.0, 19806071.0, "BPA15 1 Clean Data1.fq.gz", "0:140.52 1:140.51", "A:1513411045;C:1269789679;G:1278952098;T:1503723540;N:99909", 140, 140, null, null, 1513411045, 1269789679, 1278952098, 1503723540, 99909, "SRX19013374", "SRS16433010", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.93415, 0.93473, 0.12035, 0.11811, 0.69315, 0.69254, 0.47054, 0.47231, 105, 105, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72677, "SRR23060061", "SRX19013373", "SRS16433009", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "Control 3", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z902", "Z902", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "Control_3_Clean_Data1.fq.gz Control_3_Clean_Data2.fq.gz", "fastq fastq", 4866202369.0, 17323282.0, "Control 3 Clean Data1.fq.gz", null, null, null, null, null, null, null, null, null, null, null, "SRX19013373", "SRS16433009", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.91765, 0.91705, 0.17214, 0.16747, 0.69765, 0.69739, 0.48756, 0.49157, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72678, "SRR23060062", "SRX19013372", "SRS16433011", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "Control 2", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z901", "Z901", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "Control_2_Clean_Data1.fq.gz Control_2_Clean_Data2.fq.gz", "fastq fastq", 5265679291.0, 18766450.0, "Control 2 Clean Data1.fq.gz", null, null, null, null, null, null, null, null, null, null, null, "SRX19013372", "SRS16433011", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.92738, 0.92679, 0.17397, 0.17035, 0.69948, 0.69891, 0.48006, 0.48572, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72679, "SRR23060063", "SRX19013371", "SRS16433008", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "Control 1", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z900", "Z900", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "Control_1_Clean_Data1.fq.gz Control_1_Clean_Data2.fq.gz", "fastq fastq", 5769401401.0, 20486114.0, "Control 1 Clean Data1.fq.gz", "0:140.82 1:140.80", "A:1567930643;C:1316937376;G:1327529593;T:1556929210;N:74579", 140, 140, null, null, 1567930643, 1316937376, 1327529593, 1556929210, 74579, "SRX19013371", "SRS16433008", "SRA1573339", "yangzhou university|College of Animal Science and Technology", "yangzhou university", 2, 0.94089, 0.94089, 0.11671, 0.11386, 0.69923, 0.6994, 0.46151, 0.46472, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-01-12", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72748, "SRR23110580", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-1_S21_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-1_S21_L001_R2_001.fastq.gz", "fastq fastq", 26193525700.0, 177672099.0, "GSM6940303 r1", "0:27 1:120.43", "A:7719827835;C:5410495858;G:5661676554;T:7386218620;N:15306833", 27, 120, null, null, 7719827835, 5410495858, 5661676554, 7386218620, 15306833, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00368, 0.88598, 0.00112, 0.18215, 0.99168, 0.77757, 0.47975, 0.51393, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72749, "SRR23110581", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-2_S22_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-2_S22_L001_R2_001.fastq.gz", "fastq fastq", 20405308570.0, 138407397.0, "GSM6940303 r2", "0:27 1:120.43", "A:6066761212;C:4188427284;G:4382899879;T:5755324838;N:11895357", 27, 120, null, null, 6066761212, 4188427284, 4382899879, 5755324838, 11895357, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00368, 0.88942, 0.00119, 0.18885, 0.99184, 0.78693, 0.44927, 0.51797, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72750, "SRR23110582", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-3_S23_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-3_S23_L001_R2_001.fastq.gz", "fastq fastq", 12307572438.0, 83482484.0, "GSM6940303 r3", "0:27 1:120.43", "A:3633520237;C:2534467756;G:2656045405;T:3476373726;N:7165314", 27, 120, null, null, 3633520237, 2534467756, 2656045405, 3476373726, 7165314, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.0038, 0.8858, 0.00113, 0.18267, 0.99101, 0.77699, 0.46833, 0.52027, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72751, "SRR23110583", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-4_S24_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-4_S24_L001_R2_001.fastq.gz", "fastq fastq", 18938094183.0, 128455057.0, "GSM6940303 r4", "0:27 1:120.43", "A:5600343426;C:3891577388;G:4069279675;T:5365803260;N:11090434", 27, 120, null, null, 5600343426, 3891577388, 4069279675, 5365803260, 11090434, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00359, 0.88634, 0.00128, 0.18783, 0.99212, 0.77893, 0.48997, 0.50684, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72752, "SRR23110584", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R2_001.fastq.gz", "fastq fastq", 11012858533.0, 74696398.0, "GSM6940302 r1", "0:27 1:120.43", "A:3253931864;C:2230032555;G:2516883171;T:3003935990;N:8074953", 27, 120, null, null, 3253931864, 2230032555, 2516883171, 3003935990, 8074953, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00603, 0.89151, 0.00212, 0.18091, 0.98849, 0.79634, 0.5277, 0.52269, 27, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72753, "SRR23110585", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R2_001.fastq.gz", "fastq fastq", 10212715196.0, 69269302.0, "GSM6940302 r2", "0:27 1:120.43", "A:3014265330;C:2070878830;G:2341755898;T:2778343711;N:7471427", 27, 120, null, null, 3014265330, 2070878830, 2341755898, 2778343711, 7471427, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00554, 0.89174, 0.00191, 0.1793, 0.98884, 0.79732, 0.51857, 0.52305, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72754, "SRR23110586", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R2_001.fastq.gz", "fastq fastq", 7996112551.0, 54234020.0, "GSM6940302 r3", "0:27 1:120.44", "A:2359724282;C:1611743954;G:1830950721;T:2187871443;N:5822151", 27, 120, null, null, 2359724282, 1611743954, 1830950721, 2187871443, 5822151, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00614, 0.88908, 0.00216, 0.1836, 0.98821, 0.79547, 0.52232, 0.51954, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72755, "SRR23110587", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R2_001.fastq.gz", "fastq fastq", 11056657034.0, 74991022.0, "GSM6940302 r4", "0:27 1:120.44", "A:3246337136;C:2242556246;G:2556848463;T:3002783409;N:8131780", 27, 120, null, null, 3246337136, 2242556246, 2556848463, 3002783409, 8131780, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00621, 0.8906, 0.00194, 0.17648, 0.98762, 0.80133, 0.48802, 0.52225, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 86, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", 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