{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.platform = \"BGISEQ\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[55655, "SRR10674410", "SRX7351703", "SRS5811186", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. 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To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "Cntrol1", null, "isolate:biologocal replicate 16|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050116", "bps050116", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "Cntrol1_1.fq.gz Cntrol1_2.fq.gz", "fastq fastq", 6766663000.0, 67666630.0, "Cntrol1 1.fq.gz", "0:100 1:100", "A:1825736389;C:1564390057;G:1532835305;T:1842876742;N:824507", 100, 100, null, null, 1825736389, 1564390057, 1532835305, 1842876742, 824507, "SRX7351693", "SRS5811174", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94047, null, 0.12338, null, 0.68893, null, 0.46407, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55666, "SRR10674421", "SRX7351692", "SRS5811176", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1000 3", null, "isolate:biologocal replicate 15|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050115", "bps050115", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1000_3_1.fq.gz BPS_1000_3_2.fq.gz", "fastq fastq", 6507622200.0, 65076222.0, "BPS 1000 3 1.fq.gz", "0:100 1:100", "A:1735402948;C:1525938362;G:1493787016;T:1751945676;N:548198", 100, 100, null, null, 1735402948, 1525938362, 1493787016, 1751945676, 548198, "SRX7351692", "SRS5811176", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94304, null, 0.10593, null, 0.6842, null, 0.46348, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55667, "SRR10674422", "SRX7351691", "SRS5811173", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1000 2", null, "isolate:biologocal replicate 14|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050114", "bps050114", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1000_2_1.fq.gz BPS_1000_2_2.fq.gz", "fastq fastq", 6740712000.0, 67407120.0, "BPS 1000 2 1.fq.gz", "0:100 1:100", "A:1816870993;C:1562402111;G:1527381283;T:1833284067;N:773546", 100, 100, null, null, 1816870993, 1562402111, 1527381283, 1833284067, 773546, "SRX7351691", "SRS5811173", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94327, null, 0.11511, null, 0.70033, null, 0.4551, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55668, "SRR10674423", "SRX7351690", "SRS5811175", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1000 1", null, "isolate:biologocal replicate 13|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050113", "bps050113", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1000_1_1.fq.gz BPS_1000_1_2.fq.gz", "fastq fastq", 6727750400.0, 67277504.0, "BPS 1000 1 1.fq.gz", "0:100 1:100", "A:1803578734;C:1568712705;G:1535618959;T:1819016739;N:823263", 100, 100, null, null, 1803578734, 1568712705, 1535618959, 1819016739, 823263, "SRX7351690", "SRS5811175", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94457, null, 0.1118, null, 0.69087, null, 0.46815, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55669, "SRR10674424", "SRX7351689", "SRS5811172", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 100 3", null, "isolate:biologocal replicate 12|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050112", "bps050112", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_100_3_1.fq.gz BPS_100_3_2.fq.gz", "fastq fastq", 6962431800.0, 69624318.0, "BPS 100 3 1.fq.gz", "0:100 1:100", "A:1865300693;C:1624120289;G:1585691091;T:1886538935;N:780792", 100, 100, null, null, 1865300693, 1624120289, 1585691091, 1886538935, 780792, "SRX7351689", "SRS5811172", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94581, null, 0.10195, null, 0.68288, null, 0.47174, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55670, "SRR10674425", "SRX7351688", "SRS5811171", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 100 2", null, "isolate:biologocal replicate 11|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050111", "bps050111", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_100_2_1.fq.gz BPS_100_2_2.fq.gz", "fastq fastq", 7201035800.0, 72010358.0, "BPS 100 2 1.fq.gz", "0:100 1:100", "A:2115590854;C:1489181336;G:1459936470;T:2135514629;N:812511", 100, 100, null, null, 2115590854, 1489181336, 1459936470, 2135514629, 812511, "SRX7351688", "SRS5811171", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.90678, null, 0.29289, null, 0.70735, null, 0.49554, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55671, "SRR10674426", "SRX7351687", "SRS5811170", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 0 1 2", null, "isolate:biologocal replicate 2|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050102", "bps050102", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_0_1_2_1.fq.gz BPS_0_1_2_2.fq.gz", "fastq fastq", 7022382800.0, 70223828.0, "BPS 0 1 2 1.fq.gz", "0:100 1:100", "A:1853514579;C:1663935080;G:1635277415;T:1869136960;N:518766", 100, 100, null, null, 1853514579, 1663935080, 1635277415, 1869136960, 518766, "SRX7351687", "SRS5811170", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94712, null, 0.09313, null, 0.6814, null, 0.47256, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55672, "SRR10674427", "SRX7351686", "SRS5811167", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 0 1 1", null, "isolate:biologocal replicate 1|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050101", "bps050101", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_0_1_1_1.fq.gz BPS_0_1_1_2.fq.gz", "fastq fastq", 7013900400.0, 70139004.0, "BPS 0 1 1 1.fq.gz", "0:100 1:100", "A:1885826391;C:1629114228;G:1597181244;T:1901261511;N:517026", 100, 100, null, null, 1885826391, 1629114228, 1597181244, 1901261511, 517026, "SRX7351686", "SRS5811167", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94226, null, 0.11616, null, 0.69014, null, 0.45679, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [59480, "SRR11922874", "SRX8468588", "SRS6769276", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep6", "GSM4590772", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590772", "GSM4590772: zebrafish embryo Aldh3a1 KO rep6; Danio rerio; RNA Seq", "GSM4590772", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590772", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "12_aldh3a1----homo-48hpf-6_1.fq.gz 12_aldh3a1----homo-48hpf-6_2.fq.gz", "fastq fastq", 4660603600.0, 46606036.0, "GSM4590772 r1", "0:100 1:100", "A:1396899993;C:924291840;G:902974172;T:1436437595;N:0", 100, 100, null, null, 1396899993, 924291840, 902974172, 1436437595, 0, "SRX8468588", "SRS6769276", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.90281, null, 0.2525, null, 0.75943, null, 0.62165, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59481, "SRR11922873", "SRX8468587", "SRS6769275", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep5", "GSM4590771", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590771", "GSM4590771: zebrafish embryo Aldh3a1 KO rep5; Danio rerio; RNA Seq", "GSM4590771", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590771", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "11_aldh3a1----homo-48hpf-5_1.fq.gz 11_aldh3a1----homo-48hpf-5_2.fq.gz", "fastq fastq", 3919649800.0, 39196498.0, "GSM4590771 r1", "0:100 1:100", "A:1203194756;C:742776682;G:744133378;T:1229544984;N:0", 100, 100, null, null, 1203194756, 742776682, 744133378, 1229544984, 0, "SRX8468587", "SRS6769275", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.86745, null, 0.31349, null, 0.76702, null, 0.63864, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59482, "SRR11922872", "SRX8468586", "SRS6769274", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep4", "GSM4590770", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590770", "GSM4590770: zebrafish embryo Aldh3a1 KO rep4; Danio rerio; RNA Seq", "GSM4590770", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590770", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "10_aldh3a1----homo-48hpf-4_2.fq.gz 10_aldh3a1----homo-48hpf-4_1.fq.gz", "fastq fastq", 4549625000.0, 45496250.0, "GSM4590770 r1", "0:100 1:100", "A:1345145181;C:925949636;G:905779914;T:1372750269;N:0", 100, 100, null, null, 1345145181, 925949636, 905779914, 1372750269, 0, "SRX8468586", "SRS6769274", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.9117, null, 0.23055, null, 0.72545, null, 0.50968, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59483, "SRR11922871", "SRX8468585", "SRS6769273", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep3", "GSM4590769", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590769", "GSM4590769: zebrafish embryo Aldh3a1 KO rep3; Danio rerio; RNA Seq", "GSM4590769", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590769", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "9_aldh3a1----homo-48hpf-3_1.fq.gz 9_aldh3a1----homo-48hpf-3_2.fq.gz", "fastq fastq", 4194991600.0, 41949916.0, "GSM4590769 r1", "0:100 1:100", "A:1258296885;C:833884600;G:816600639;T:1286209476;N:0", 100, 100, null, null, 1258296885, 833884600, 816600639, 1286209476, 0, "SRX8468585", "SRS6769273", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.89574, null, 0.28139, null, 0.73397, null, 0.56688, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59484, "SRR11922870", "SRX8468584", "SRS6769272", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep2", "GSM4590768", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590768", "GSM4590768: zebrafish embryo Aldh3a1 KO rep2; Danio rerio; RNA Seq", "GSM4590768", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590768", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "8_aldh3a1----homo-48hpf-2_1.fq.gz 8_aldh3a1----homo-48hpf-2_2.fq.gz", "fastq fastq", 5097901600.0, 50979016.0, "GSM4590768 r1", "0:100 1:100", "A:1487281075;C:1055394796;G:1035616985;T:1519608744;N:0", 100, 100, null, null, 1487281075, 1055394796, 1035616985, 1519608744, 0, "SRX8468584", "SRS6769272", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.92556, null, 0.18622, null, 0.73026, null, 0.5187, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59485, "SRR11922869", "SRX8468583", "SRS6769271", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep1", "GSM4590767", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590767", "GSM4590767: zebrafish embryo Aldh3a1 KO rep1; Danio rerio; RNA Seq", "GSM4590767", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590767", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "7_aldh3a1----homo-48hpf-1_1.fq.gz 7_aldh3a1----homo-48hpf-1_2.fq.gz", "fastq fastq", 5075421000.0, 50754210.0, "GSM4590767 r1", "0:100 1:100", "A:1523744143;C:1008915874;G:985443760;T:1557317223;N:0", 100, 100, null, null, 1523744143, 1008915874, 985443760, 1557317223, 0, "SRX8468583", "SRS6769271", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.90167, null, 0.27915, null, 0.75879, null, 0.6673, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59486, "SRR11922868", "SRX8468582", "SRS6769270", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep5", "GSM4590766", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590766", "GSM4590766: zebrafish embryo wildtype rep5; Danio rerio; RNA Seq", "GSM4590766", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590766", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "6_aldh3a1+-+-wt-48hpf-R_1.fq.gz 6_aldh3a1+-+-wt-48hpf-R_2.fq.gz", "fastq fastq", 5097636600.0, 50976366.0, "GSM4590766 r1", "0:100 1:100", "A:1402424015;C:1146863463;G:1121174200;T:1427174922;N:0", 100, 100, null, null, 1402424015, 1146863463, 1121174200, 1427174922, 0, "SRX8468582", "SRS6769270", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.95115, null, 0.09816, null, 0.69781, null, 0.46194, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59487, "SRR11922867", "SRX8468581", "SRS6769269", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep4", "GSM4590765", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590765", "GSM4590765: zebrafish embryo wildtype rep4; Danio rerio; RNA Seq", "GSM4590765", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590765", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "4_aldh3a1+-+-wt-48hpf-4_1.fq.gz 4_aldh3a1+-+-wt-48hpf-4_2.fq.gz", "fastq fastq", 4847250800.0, 48472508.0, "GSM4590765 r1", "0:100 1:100", "A:1351516729;C:1070410976;G:1050113082;T:1375210013;N:0", 100, 100, null, null, 1351516729, 1070410976, 1050113082, 1375210013, 0, "SRX8468581", "SRS6769269", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.94418, null, 0.12404, null, 0.69374, null, 0.49948, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59488, "SRR11922866", "SRX8468580", "SRS6769268", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep3", "GSM4590764", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590764", "GSM4590764: zebrafish embryo wildtype rep3; Danio rerio; RNA Seq", "GSM4590764", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590764", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "3_aldh3a1+-+-wt-48hpf-3_1.fq.gz 3_aldh3a1+-+-wt-48hpf-3_2.fq.gz", "fastq fastq", 5083417400.0, 50834174.0, "GSM4590764 r1", "0:100 1:100", "A:1375006484;C:1168556107;G:1139277849;T:1400576960;N:0", 100, 100, null, null, 1375006484, 1168556107, 1139277849, 1400576960, 0, "SRX8468580", "SRS6769268", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.95419, null, 0.09201, null, 0.69209, null, 0.48244, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59489, "SRR11922865", "SRX8468579", "SRS6769267", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep2", "GSM4590763", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590763", "GSM4590763: zebrafish embryo wildtype rep2; Danio rerio; RNA Seq", "GSM4590763", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590763", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "2_aldh3a1+-+-wt-48hpf-2_1.fq.gz 2_aldh3a1+-+-wt-48hpf-2_2.fq.gz", "fastq fastq", 5089646400.0, 50896464.0, "GSM4590763 r1", "0:100 1:100", "A:1384714450;C:1161015785;G:1138313445;T:1405602720;N:0", 100, 100, null, null, 1384714450, 1161015785, 1138313445, 1405602720, 0, "SRX8468579", "SRS6769267", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.95309, null, 0.09301, null, 0.69798, null, 0.48524, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59490, "SRR11922864", "SRX8468578", "SRS6769266", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep1", "GSM4590762", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590762", "GSM4590762: zebrafish embryo wildtype rep1; Danio rerio; RNA Seq", "GSM4590762", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590762", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "1_aldh3a1+-+-wt-48hpf-1_1.fq.gz 1_aldh3a1+-+-wt-48hpf-1_2.fq.gz", "fastq fastq", 5098267400.0, 50982674.0, "GSM4590762 r1", "0:100 1:100", "A:1406329756;C:1147290302;G:1118206731;T:1426440611;N:0", 100, 100, null, null, 1406329756, 1147290302, 1118206731, 1426440611, 0, "SRX8468578", "SRS6769266", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.95039, null, 0.10482, null, 0.69641, null, 0.47979, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [65852, "SRR15657174", "SRX11954177", "SRS9963999", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Cu 0.156uM 96hpf", "GSM5543529", null, "tissue:embryo  Cu 0.156uM 96hpf|cell type:embryos at 96hpf whose parents were exposed to 0.156\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Cu 0.156uM 96hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Cu 0.156uM 96hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 96hpf hours post  fertilization|treatment:embryos whose parents were exposed to 0.156\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543529", "GSM5543529: embryo Cu 0.156uM 96hpf; Danio rerio; RNA Seq", "GSM5543529", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Cu_0.156uM_96hpf_R1.fastq.gz Cu_0.156uM_96hpf_R2.fastq.gz", "fastq fastq", 7167443000.0, 71674430.0, "GSM5543529 r1", "0:100 1:100", "A:1930084120;C:1646651059;G:1623549050;T:1966203424;N:955347", 100, 100, null, null, 1930084120, 1646651059, 1623549050, 1966203424, 955347, "SRX11954177", "SRS9963999", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.94339, null, 0.113, null, 0.6549, null, 0.4857, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [65853, "SRR15657173", "SRX11954176", "SRS9963998", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Cu 0.156uM 24hpf", "GSM5543528", null, "tissue:embryo  Cu 0.156uM 24hpf|cell type:embryos at 24hpf whose parents were exposed to 0.156\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Cu 0.156uM 24hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Cu 0.156uM 24hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 24hpf hours post  fertilization|treatment:embryos whose parents were exposed to 0.156\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543528", "GSM5543528: embryo Cu 0.156uM 24hpf; Danio rerio; RNA Seq", "GSM5543528", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Cu_0.156uM_24hpf_R1.fastq.gz Cu_0.156uM_24hpf_R2.fastq.gz", "fastq fastq", 7164832400.0, 71648324.0, "GSM5543528 r1", "0:100 1:100", "A:1929135591;C:1646939515;G:1617401036;T:1970900148;N:456110", 100, 100, null, null, 1929135591, 1646939515, 1617401036, 1970900148, 456110, "SRX11954176", "SRS9963998", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.94344, null, 0.10713, null, 0.68919, null, 0.47118, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [65854, "SRR15657172", "SRX11954175", "SRS9963997", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Cu 0.078uM 96hpf", "GSM5543527", null, "tissue:embryo  Cu 0.078uM 96hpf|cell type:embryos at 96hpf whose parents were exposed to 0.078\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Cu 0.078uM 96hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Cu 0.078uM 96hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 96hpf hours post  fertilization|treatment:embryos whose parents were exposed to 0.078\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543527", "GSM5543527: embryo Cu 0.078uM 96hpf; Danio rerio; RNA Seq", "GSM5543527", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Cu_0.078uM_96hpf_R1.fastq.gz Cu_0.078uM_96hpf_R2.fastq.gz", "fastq fastq", 7135774800.0, 71357748.0, "GSM5543527 r1", "0:100 1:100", "A:1928230196;C:1633490990;G:1605871113;T:1967776814;N:405687", 100, 100, null, null, 1928230196, 1633490990, 1605871113, 1967776814, 405687, "SRX11954175", "SRS9963997", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.94191, null, 0.11803, null, 0.65614, null, 0.48225, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [65855, "SRR15657171", "SRX11954174", "SRS9963995", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Cu 0.078uM 24hpf", "GSM5543526", null, "tissue:embryo  Cu 0.078uM 24hpf|cell type:embryos at 24hpf whose parents were exposed to 0.078\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Cu 0.078uM 24hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Cu 0.078uM 24hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 24hpf hours post  fertilization|treatment:embryos whose parents were exposed to 0.078\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543526", "GSM5543526: embryo Cu 0.078uM 24hpf; Danio rerio; RNA Seq", "GSM5543526", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Cu_0.078uM_24hpf_R1.fastq.gz Cu_0.078uM_24hpf_R2.fastq.gz", "fastq fastq", 6934019600.0, 69340196.0, "GSM5543526 r1", "0:100 1:100", "A:1865548284;C:1597354050;G:1569395022;T:1901304271;N:417973", 100, 100, null, null, 1865548284, 1597354050, 1569395022, 1901304271, 417973, "SRX11954174", "SRS9963995", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.94389, null, 0.10356, null, 0.68726, null, 0.47794, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [65856, "SRR15657170", "SRX11954173", "SRS9963996", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Control 96hpf", "GSM5543525", null, "tissue:embryo  Control 96hpf|cell type:embryos at 96hpf whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Control 96hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Control 96hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 96hpf hours post  fertilization|treatment:embryos whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543525", "GSM5543525: embryo Control 96hpf; Danio rerio; RNA Seq", "GSM5543525", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Control_96hpf_R1.fastq.gz Control_96hpf_R2.fastq.gz", "fastq fastq", 6698614400.0, 66986144.0, "GSM5543525 r1", "0:100 1:100", "A:1816763075;C:1526218454;G:1496202651;T:1858550518;N:879702", 100, 100, null, null, 1816763075, 1526218454, 1496202651, 1858550518, 879702, "SRX11954173", "SRS9963996", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.93836, null, 0.12432, null, 0.65504, null, 0.47564, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [65857, "SRR15657169", "SRX11954172", "SRS9963994", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Control 24hpf", "GSM5543524", null, "tissue:embryo  Control 24hpf|cell type:embryos at 24hpf whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Control 24hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Control 24hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 24hpf hours post  fertilization|treatment:embryos whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543524", "GSM5543524: embryo Control 24hpf; Danio rerio; RNA Seq", "GSM5543524", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Control_24hpf_R1.fastq.gz Control_24hpf_R2.fastq.gz", "fastq fastq", 6911559200.0, 69115592.0, "GSM5543524 r1", "0:100 1:100", "A:1858569189;C:1592355971;G:1564572369;T:1895593185;N:468486", 100, 100, null, null, 1858569189, 1592355971, 1564572369, 1895593185, 468486, "SRX11954172", "SRS9963994", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.93745, null, 0.09795, null, 0.69059, null, 0.48209, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 35, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], 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